├── QMMM-Tutorial-Handbook.pdf ├── QMMM-Tutorial.pptx ├── egfp ├── 4eul.pdb ├── amber03_gfp.ff │ ├── FF.dat │ ├── aminoacids-NA.dat │ ├── aminoacids.dat │ ├── atommass.dat │ ├── bromacs.dat │ ├── ca-shift.dat │ ├── cb-shift.dat │ ├── co-shift.dat │ ├── dgsolv.dat │ ├── edissoc.dat │ ├── electroneg.dat │ ├── elements.dat │ ├── ffamber03-c.tdb │ ├── ffamber03-n.tdb │ ├── ffamber03.atp │ ├── ffamber03.hdb │ ├── ffamber03.rtp │ ├── ffamber03bon.itp │ ├── ffamber03nb.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── gurgle.dat │ ├── ha-shift.dat │ ├── highway.dat │ ├── ions.itp │ ├── links.dat │ ├── phbres.dat │ ├── pyr.dat │ ├── random.dat │ ├── refi_aa.dat │ ├── spc216.gro │ ├── specbond.dat │ ├── surface.dat │ ├── tip3p.itp │ ├── tip4p.itp │ ├── vdwradii.dat │ ├── watermodels.dat │ └── xlateat.dat ├── conv.py ├── em.mdp ├── md-mm-nvt.mdp ├── md-qmmm-nvt.mdp ├── md-qmmm-spec.mdp ├── residuetypes.dat ├── run-em.sh ├── run-mm-nvt.sh ├── run-qmmm-nvt.sh ├── run-qmmm-spec.sh └── xlateat.dat ├── nma ├── atommass.dat ├── charmm36-mar2019.ff │ ├── atomtypes.atp │ ├── cmap.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── gb.itp │ ├── ions.itp │ ├── merged.arn │ ├── merged.c.tdb │ ├── merged.hdb │ ├── merged.n.tdb │ ├── merged.r2b │ ├── merged.rtp │ ├── merged.vsd │ ├── nbfix.itp │ ├── old_c36_cmap.itp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ └── watermodels.dat ├── elements.dat ├── em.mdp ├── md-nvt.mdp ├── nma.pdb ├── residuetypes.dat ├── run-em.sh ├── run-nvt.sh ├── spc216.gro ├── specbond.dat ├── vdwradii.dat └── xlateat.dat └── stilbene_vacuum ├── BASIS_MOLOPT ├── POTENTIAL ├── amber14sb_OL15.ff ├── Makefile.am ├── Makefile.in ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.doc ├── forcefield.itp ├── gbsa.itp ├── ions.itp ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── conf.gro ├── eq_gro ├── md-equilb1.gro ├── md-equilb10.gro ├── md-equilb11.gro ├── md-equilb12.gro ├── md-equilb13.gro ├── md-equilb14.gro ├── md-equilb15.gro ├── md-equilb16.gro ├── md-equilb17.gro ├── md-equilb18.gro ├── md-equilb19.gro ├── md-equilb2.gro ├── md-equilb20.gro ├── md-equilb21.gro ├── md-equilb22.gro ├── md-equilb23.gro ├── md-equilb24.gro ├── md-equilb25.gro ├── md-equilb26.gro ├── md-equilb27.gro ├── md-equilb28.gro ├── md-equilb29.gro ├── md-equilb3.gro ├── md-equilb30.gro ├── md-equilb4.gro ├── md-equilb5.gro ├── md-equilb6.gro ├── md-equilb7.gro ├── md-equilb8.gro └── md-equilb9.gro ├── index.ndx ├── profile-100fs ├── histo.xvg ├── profile-10ps.xvg ├── profile.xvg ├── pullx-files.dat ├── pullx1.xvg ├── pullx10.xvg ├── pullx11.xvg ├── pullx12.xvg ├── pullx13.xvg ├── pullx14.xvg ├── pullx15.xvg ├── pullx16.xvg ├── pullx17.xvg ├── pullx18.xvg ├── pullx19.xvg ├── pullx2.xvg ├── pullx20.xvg ├── pullx21.xvg ├── pullx22.xvg ├── pullx23.xvg ├── pullx24.xvg ├── pullx25.xvg ├── pullx26.xvg ├── pullx27.xvg ├── pullx28.xvg ├── pullx29.xvg ├── pullx3.xvg ├── pullx30.xvg ├── pullx4.xvg ├── pullx5.xvg ├── pullx6.xvg ├── pullx7.xvg ├── pullx8.xvg ├── pullx9.xvg ├── stilbene1.tpr ├── stilbene10.tpr ├── stilbene11.tpr ├── stilbene12.tpr ├── stilbene13.tpr ├── stilbene14.tpr ├── stilbene15.tpr ├── stilbene16.tpr ├── stilbene17.tpr ├── stilbene18.tpr ├── stilbene19.tpr ├── stilbene2.tpr ├── stilbene20.tpr ├── stilbene21.tpr ├── stilbene22.tpr ├── stilbene23.tpr ├── stilbene24.tpr ├── stilbene25.tpr ├── stilbene26.tpr ├── stilbene27.tpr ├── stilbene28.tpr ├── stilbene29.tpr ├── stilbene3.tpr ├── stilbene30.tpr ├── stilbene4.tpr ├── stilbene5.tpr ├── stilbene6.tpr ├── stilbene7.tpr ├── stilbene8.tpr ├── stilbene9.tpr └── tpr-files.dat ├── qmmm_md_umbrella.mdp ├── residuetypes.dat ├── run.sh └── topol.top /QMMM-Tutorial-Handbook.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioexcel/gromacs-2022-cp2k-tutorial/de2d4e83c20cb350ea3b962ef1d5d017e2c95d33/QMMM-Tutorial-Handbook.pdf -------------------------------------------------------------------------------- /QMMM-Tutorial.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioexcel/gromacs-2022-cp2k-tutorial/de2d4e83c20cb350ea3b962ef1d5d017e2c95d33/QMMM-Tutorial.pptx -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/FF.dat: -------------------------------------------------------------------------------- 1 | 11 2 | ffG43a1 GROMOS96 43a1 force field 3 | ffG43a2 GROMOS96 43a2 force field (improved alkane dihedrals) 4 | ffG45a3 GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 5 | ffG53a5 GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 6 | ffG53a6 GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 7 | ffoplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 8 | ffgmx [DEPRECATED] Gromacs force field (see manual) 9 | ffgmx2 [DEPRECATED] Gromacs force field with hydrogens for NMR 10 | ffencadv Encad all-atom force field, using scaled-down vacuum charges 11 | ffencads Encad all-atom force field, using full solvent charges 12 | ffamber03 AMBER 13 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/aminoacids-NA.dat: -------------------------------------------------------------------------------- 1 | 142 2 | ABU 3 | ACE 4 | ACE 5 | AIB 6 | ALA 7 | ARG 8 | ARGN 9 | ASH 10 | ASN 11 | ASN1 12 | ASP 13 | ASP1 14 | ASPH 15 | CALA 16 | CARG 17 | CASN 18 | CASP 19 | CCYN 20 | CCYX 21 | CGLN 22 | CGLU 23 | CGLY 24 | CHID 25 | CHIE 26 | CHIP 27 | CILE 28 | CLEU 29 | CLYP 30 | CMET 31 | CPHE 32 | CPRO 33 | CSER 34 | CTHR 35 | CTRP 36 | CTYR 37 | CVAL 38 | CYM 39 | CYN 40 | CYS 41 | CYS1 42 | CYS2 43 | CYSH 44 | CYX 45 | DA 46 | DA3 47 | DA5 48 | DAB 49 | DALA 50 | DAN 51 | DC 52 | DC3 53 | DC5 54 | DCN 55 | DG 56 | DG3 57 | DG5 58 | DGN 59 | DT 60 | DT3 61 | DT5 62 | DTN 63 | GLH 64 | GLN 65 | GLU 66 | GLUH 67 | GLY 68 | HID 69 | HIE 70 | HIP 71 | HIS 72 | HIS1 73 | HISA 74 | HISB 75 | HISH 76 | HYP 77 | ILE 78 | LEU 79 | LYN 80 | LYP 81 | LYS 82 | LYSH 83 | MELEU 84 | MET 85 | MEVAL 86 | NAC 87 | NALA 88 | NARG 89 | NASN 90 | NASP 91 | NCYN 92 | NCYX 93 | NGLN 94 | NGLU 95 | NGLY 96 | NH2 97 | NHE 98 | NHID 99 | NHIE 100 | NHIP 101 | NILE 102 | NLEU 103 | NLYP 104 | NME 105 | NMET 106 | NPHE 107 | NPRO 108 | NSER 109 | NTHR 110 | NTRP 111 | NTYR 112 | NVAL 113 | ORN 114 | PHE 115 | PHEH 116 | PHEU 117 | PHL 118 | PRO 119 | RA 120 | RA3 121 | RA5 122 | RAN 123 | RC 124 | RC3 125 | RC5 126 | RCN 127 | RG 128 | RG3 129 | RG5 130 | RGN 131 | RU 132 | RU3 133 | RU5 134 | RUN 135 | SER 136 | THR 137 | TRP 138 | TRPH 139 | TRPU 140 | TYR 141 | TYRH 142 | TYRU 143 | VAL 144 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/aminoacids.dat: -------------------------------------------------------------------------------- 1 | 54 2 | ABU 3 | ACE 4 | AIB 5 | ALA 6 | ARG 7 | ARGN 8 | ASN 9 | ASN1 10 | ASP 11 | ASP1 12 | ASPH 13 | CYS 14 | CYM 15 | CYN 16 | CYS1 17 | CYS2 18 | CYSH 19 | DALA 20 | GLN 21 | GLU 22 | GLUH 23 | GLY 24 | HIS 25 | HIS1 26 | HISA 27 | HISB 28 | HISH 29 | HYP 30 | ILE 31 | LEU 32 | LYS 33 | LYSH 34 | MELEU 35 | MET 36 | MEVAL 37 | NAC 38 | NH2 39 | NTHR 40 | PHE 41 | PHEH 42 | PHEU 43 | PHL 44 | PRO 45 | SER 46 | THR 47 | TRP 48 | TRPH 49 | TRPU 50 | TYR 51 | TYRH 52 | TYRU 53 | VAL 54 | SYG 55 | TYG 56 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/bromacs.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioexcel/gromacs-2022-cp2k-tutorial/de2d4e83c20cb350ea3b962ef1d5d017e2c95d33/egfp/amber03_gfp.ff/bromacs.dat -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/ca-shift.dat: -------------------------------------------------------------------------------- 1 | 18 18 2 | -2.35 -2.39 -2.36 -2.23 -1.98 -1.64 -1.26 -0.93 -0.68 -0.51 -0.38 -0.09 0.13 -0.15 -1.09 -1.88 -2.13 -2.26 3 | -2.33 -2.36 -2.32 -2.18 -1.91 -1.54 -1.12 -0.75 -0.45 -0.27 -0.25 -0.54 -1.12 -1.57 -1.89 -2.04 -2.15 -2.25 4 | -2.28 -2.30 -2.25 -2.11 -1.83 -1.44 -1.00 -0.58 -0.25 -0.05 -0.05 -0.64 -1.50 -1.86 -1.99 -2.00 -2.09 -2.20 5 | -2.19 -2.22 -2.18 -2.03 -1.76 -1.37 -0.92 -0.48 -0.12 0.12 0.08 -0.48 -0.98 -1.31 -1.54 -1.65 -1.89 -2.09 6 | -2.07 -2.13 -2.10 -1.96 -1.70 -1.33 -0.90 -0.47 -0.08 0.19 0.15 -0.02 -0.10 -0.23 -0.41 -0.74 -1.40 -1.86 7 | -1.90 -2.01 -1.99 -1.85 -1.60 -1.26 -0.88 -0.49 -0.10 0.19 0.29 0.39 0.49 0.56 0.63 0.44 -0.62 -1.52 8 | -1.65 -1.77 -1.68 -1.45 -1.14 -0.81 -0.50 -0.19 0.10 0.31 0.47 0.63 0.78 0.91 1.06 1.10 0.12 -1.14 9 | -1.34 -1.32 -1.03 -0.60 -0.16 0.24 0.59 0.88 1.04 0.81 0.64 0.78 0.94 1.09 1.26 1.37 0.59 -0.83 10 | -1.02 -0.85 -0.41 0.13 0.66 1.11 1.46 1.72 1.87 1.63 0.94 0.88 1.05 1.23 1.42 1.54 0.81 -0.63 11 | -0.65 -0.47 0.07 0.70 1.26 1.69 1.99 2.19 2.31 2.27 1.56 1.03 1.13 1.34 1.56 1.71 0.98 -0.28 12 | -0.22 -0.10 0.51 1.20 1.73 2.08 2.32 2.47 2.56 2.59 2.28 1.40 1.26 1.44 1.68 1.89 1.33 0.28 13 | 0.12 0.20 0.87 1.56 2.04 2.33 2.51 2.63 2.71 2.75 2.69 2.14 1.58 1.51 1.71 2.06 1.73 0.76 14 | 0.16 0.26 1.03 1.75 2.20 2.46 2.62 2.72 2.79 2.83 2.88 2.69 1.93 1.44 1.56 2.10 1.93 0.90 15 | -0.19 -0.03 0.86 1.70 2.20 2.48 2.64 2.75 2.81 2.85 2.90 2.69 1.90 1.25 1.28 1.95 1.82 0.62 16 | -0.99 -0.85 0.00 1.05 1.80 2.24 2.50 2.64 2.72 2.72 2.64 2.30 1.69 1.14 1.09 1.57 1.08 -0.31 17 | -1.91 -1.92 -1.62 -0.93 -0.02 0.82 1.43 1.83 2.05 2.09 1.98 1.75 1.40 1.13 1.07 0.74 -0.71 -1.62 18 | -2.24 -2.30 -2.25 -2.07 -1.73 -1.28 -0.82 -0.40 -0.02 0.48 1.06 1.18 1.09 1.06 0.91 -0.44 -1.75 -2.10 19 | -2.33 -2.38 -2.36 -2.23 -2.00 -1.67 -1.33 -1.04 -0.79 -0.52 0.05 0.59 0.77 0.80 0.20 -1.40 -2.04 -2.22 20 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/cb-shift.dat: -------------------------------------------------------------------------------- 1 | 18 18 2 | 2.86 3.04 2.96 2.61 2.10 1.67 1.47 1.41 1.34 1.18 0.93 0.27 0.28 0.81 1.61 1.94 2.10 2.49 3 | 3.00 3.13 2.99 2.61 2.05 1.52 1.18 1.00 0.86 0.76 0.81 1.10 1.71 2.35 2.58 2.25 2.27 2.66 4 | 2.93 3.01 2.86 2.47 1.93 1.37 0.99 0.76 0.61 0.51 0.52 0.80 1.52 2.21 2.58 2.34 2.30 2.65 5 | 2.69 2.76 2.60 2.24 1.72 1.21 0.84 0.60 0.43 0.23 -0.27 -0.25 0.47 1.22 1.89 1.82 1.90 2.39 6 | 2.32 2.42 2.27 1.92 1.44 0.99 0.65 0.42 0.15 -0.46 -1.68 -1.46 -0.82 -0.19 0.43 0.41 0.86 1.85 7 | 1.90 2.03 1.88 1.51 1.03 0.63 0.36 0.13 -0.34 -1.71 -2.58 -2.27 -1.87 -1.51 -1.20 -1.11 -0.16 1.25 8 | 1.47 1.52 1.31 0.87 0.41 0.12 0.00 -0.13 -0.89 -2.63 -2.86 -2.58 -2.33 -2.17 -2.07 -1.95 -0.55 0.94 9 | 1.06 1.00 0.79 0.45 0.13 -0.03 -0.05 -0.06 -0.71 -2.77 -2.95 -2.69 -2.50 -2.39 -2.34 -2.25 -0.58 0.84 10 | 0.97 0.96 0.80 0.51 0.22 0.06 0.00 -0.02 -0.20 -1.86 -2.92 -2.74 -2.56 -2.45 -2.39 -2.28 -0.56 0.83 11 | 1.07 1.15 0.94 0.57 0.22 0.02 -0.06 -0.09 -0.13 -0.58 -2.43 -2.71 -2.55 -2.42 -2.31 -2.04 -0.21 0.82 12 | 1.05 1.25 1.03 0.56 0.17 -0.04 -0.13 -0.15 -0.15 -0.20 -1.16 -2.42 -2.36 -2.18 -1.96 -1.27 0.36 0.77 13 | 0.98 1.22 1.05 0.55 0.15 -0.06 -0.14 -0.16 -0.14 -0.13 -0.43 -1.60 -1.75 -1.61 -1.23 -0.09 0.81 0.80 14 | 0.96 1.10 0.99 0.58 0.20 -0.02 -0.11 -0.13 -0.12 -0.10 -0.30 -0.96 -1.00 -0.88 -0.43 0.69 1.15 0.94 15 | 0.96 0.92 0.84 0.60 0.30 0.08 -0.04 -0.08 -0.08 -0.05 -0.28 -0.70 -0.57 -0.38 0.05 1.01 1.38 1.13 16 | 0.98 0.79 0.72 0.64 0.47 0.27 0.11 0.03 0.00 0.02 -0.30 -0.65 -0.55 -0.39 -0.08 0.80 1.45 1.28 17 | 1.43 1.36 1.32 1.25 1.13 0.96 0.75 0.57 0.43 0.25 -0.42 -0.68 -0.58 -0.44 -0.23 0.38 1.46 1.55 18 | 2.02 2.17 2.23 2.11 1.88 1.72 1.73 1.85 1.93 1.49 -0.28 -0.53 -0.40 -0.23 0.01 0.75 1.73 1.88 19 | 2.51 2.72 2.74 2.48 2.08 1.80 1.75 1.87 1.96 1.76 0.48 -0.28 -0.17 0.06 0.47 1.45 1.93 2.21 20 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/co-shift.dat: -------------------------------------------------------------------------------- 1 | 18 18 2 | -2.18 -2.05 -1.89 -1.59 -1.14 -0.80 -0.73 -0.80 -0.81 -0.39 0.05 -0.69 -0.96 -0.97 -1.27 -2.74 -2.55 -2.33 3 | -2.19 -2.07 -1.91 -1.64 -1.25 -0.87 -0.68 -0.71 -0.85 -0.61 -0.18 -1.00 -1.36 -1.37 -1.62 -2.75 -2.56 -2.33 4 | -2.04 -2.05 -1.91 -1.65 -1.28 -0.84 -0.57 -0.66 -0.99 -0.99 -0.68 -1.29 -1.40 -1.40 -1.45 -2.20 -2.06 -1.97 5 | -1.88 -2.04 -1.93 -1.69 -1.34 -0.92 -0.63 -0.72 -1.14 -1.36 -1.23 -1.40 -1.41 -1.41 -1.41 -1.46 -1.40 -1.56 6 | -2.00 -2.14 -2.00 -1.76 -1.47 -1.13 -0.83 -0.80 -1.23 -1.63 -1.62 -1.53 -1.50 -1.50 -1.51 -1.31 -1.18 -1.56 7 | -2.40 -2.42 -2.20 -1.83 -1.48 -1.17 -0.84 -0.74 -1.38 -1.71 -1.59 -1.47 -1.44 -1.50 -1.60 -1.52 -1.56 -2.06 8 | -2.48 -2.38 -2.02 -1.34 -0.72 -0.42 -0.24 -0.38 -1.45 -1.68 -1.50 -1.36 -1.33 -1.42 -1.59 -1.55 -1.56 -2.08 9 | -1.63 -1.20 -0.74 -0.27 0.06 0.25 0.39 0.44 -0.60 -1.63 -1.52 -1.37 -1.34 -1.45 -1.63 -1.58 -1.52 -1.69 10 | -0.32 -0.16 -0.05 0.17 0.46 0.81 1.13 1.32 1.24 -0.97 -1.61 -1.50 -1.47 -1.56 -1.72 -1.66 -1.50 -1.13 11 | -0.47 -0.44 -0.03 0.57 1.13 1.57 1.79 1.84 1.83 1.28 -1.42 -1.65 -1.64 -1.69 -1.79 -1.74 -1.22 -0.62 12 | -0.61 -0.53 0.04 1.05 1.71 1.99 2.06 2.05 2.01 1.93 0.40 -1.66 -1.73 -1.75 -1.78 -1.55 -0.86 -0.72 13 | -0.71 -0.56 0.06 1.26 1.90 2.10 2.13 2.10 2.04 1.96 1.64 -1.12 -1.69 -1.72 -1.73 -1.14 -0.92 -0.83 14 | -0.79 -0.66 -0.21 1.03 1.83 2.07 2.12 2.11 2.04 1.93 1.71 0.68 -0.01 -0.59 -1.09 -1.02 -0.96 -0.90 15 | -0.75 -0.76 -0.72 0.31 1.52 1.94 2.07 2.09 2.05 1.92 1.32 0.86 0.75 0.55 0.17 -0.85 -0.98 -0.88 16 | -0.29 -0.29 -0.53 -0.46 0.71 1.56 1.88 2.01 2.03 1.77 0.91 0.71 0.46 0.05 -0.38 -0.71 -0.96 -0.60 17 | -1.00 -0.54 -0.43 -0.73 -0.74 -0.19 0.38 0.78 1.10 1.05 0.66 0.34 -0.10 -0.49 -0.73 -0.92 -1.38 -1.33 18 | -1.76 -1.71 -1.53 -1.30 -0.95 -0.79 -0.93 -1.12 -1.16 -0.25 0.20 -0.24 -0.59 -0.77 -0.86 -1.24 -1.66 -1.69 19 | -2.01 -1.99 -1.86 -1.51 -0.95 -0.66 -0.75 -0.96 -1.03 -0.56 -0.24 -0.66 -0.81 -0.87 -0.92 -2.05 -2.11 -2.01 20 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/dgsolv.dat: -------------------------------------------------------------------------------- 1 | ; 2 | ; Atomic solvation parameters: i.e. free energy of solvation (kcal/mol) per 3 | ; unit of solvent exposed area (A^2). The atomnames are really atomtypes! 4 | ; 5 | ; Data from Eisenberg and McLachlan, Nature 319 (1986), 199-203 6 | ; These numbers are for united atoms. 7 | ; 8 | ; Read this only using the function get_dgsolv (include "atomprop.h") 9 | ; 10 | ??? C 0.016 11 | ??? N -0.006 12 | ??? O -0.006 13 | ; In the original paper by Eisenberg and McLachlan, GLU and ASP sidechains 14 | ; have one negative oxygen atom (OM) and normal (O). The OM is then selected 15 | ; to be the most solvent accessible one. Since in a simulation 16 | ; such sidechains will usually flip around anyway we average the constants 17 | ; here, so OM' = (OM + O)/2 18 | ;??? OM -0.024 19 | ??? OM -0.015 20 | ??? NL -0.050 21 | ??? S 0.021 22 | ??? H 0.0 23 | ; Right now the data from the ref below are *not* used! 24 | ; Data are taken from Wang et al. J Phys Chem B 105 (2001) p 5055-5067 25 | ; to be more precise this is from table 4, model 4 26 | ; 27 | ;??? C3 0.0117970 28 | ;??? C2 -0.0183314 29 | ;??? C1 -0.4449764 30 | ;??? CT 0.0697875 31 | ;??? CA -0.0480703 32 | ;??? CD2 -0.1236206 33 | ;??? CD1 -0.1226437 34 | ;??? CD 0.0246029 35 | ;??? CS -0.0061025 36 | ;??? CO -0.1178312 37 | ;??? CN 0.0208413 38 | ;??? F 0.0194227 39 | ;??? Cl -0.0015111 40 | ;??? Br -0.0068335 41 | ;??? I -0.0066410 42 | ;??? HCT3 -0.0061394 43 | ;??? HCT2 -0.0365374 44 | ;??? HC -0.0365374 45 | ;??? HCT1 -0.0215288 46 | ;??? HCT 0.0062124 47 | ;??? HCD2 0.1459805 48 | ;??? HCD1 0.0820232 49 | ;??? HCD 0.1036663 50 | ;??? HCA 0.0220654 51 | ;??? HCS 0.0100682 52 | ;??? HO -0.0029297 53 | ;??? HN -0.2363502 54 | ;??? HS 0.0377756 55 | ;??? OA -0.3006240 56 | ;??? OC -0.0816844 57 | ;??? O -0.1357120 58 | ;??? OS 0.1176048 59 | ;??? OOH -0.1421025 60 | ;??? SH -0.0372476 61 | ;??? SS -0.0121603 62 | ;??? SP -0.0477491 63 | ;??? NS -0.1143369 64 | ;??? ND2 -0.3270664 65 | ;??? ND3 -0.4072273 66 | ;??? NO 0.7646976 67 | ;??? NH2 0.5234891 68 | ;??? NH1 -0.3474580 69 | ;??? N -0.4713683 70 | ;??? NTH2 0.2720645 71 | ;??? NTH 0.0325122 72 | ;??? NT -0.3476829 73 | ;??? P3 1.5160293 74 | ;??? P4 -0.2509340 75 | ;??? O- -1.2154901 76 | ;??? OA- -2.1887474 77 | ;??? S- -1.1141940 78 | ;??? HN+ -1.3254553 79 | ;??? NT+ 6.2614711 80 | ;??? ND+ -5.7053672 81 | ;??? N+ 2.6350040 82 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/edissoc.dat: -------------------------------------------------------------------------------- 1 | C O 743 2 | C OA 360 3 | C OM 551 4 | C C 348 5 | C H 412 6 | C N 305 7 | C S 259 8 | C CB 348 9 | CB CB 480 10 | CR5 CR5 480 11 | CR6 CR6 480 12 | NR5 CR5 459 13 | N H 388 14 | O H 463 15 | S S 264 16 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/electroneg.dat: -------------------------------------------------------------------------------- 1 | ??? H 2.1 2 | ??? Li 1.0 3 | ??? Be 1.5 4 | ??? B 2.0 5 | ??? C 2.5 6 | ??? N 3.0 7 | ??? O 3.5 8 | ??? F 4.0 9 | ??? Na 0.9 10 | ??? Mg 1.2 11 | ??? Al 1.5 12 | ??? Si 1.8 13 | ??? P 2.1 14 | ??? S 2.5 15 | ??? Cl 3.0 16 | ??? K 0.8 17 | ??? Ca 1.0 18 | ??? Sc 1.3 19 | ??? Ti 1.5 20 | ??? V 1.6 21 | ??? Cr 1.6 22 | ??? Mn 1.5 23 | ??? Fe 1.8 24 | ??? Co 1.9 25 | ??? Ni 1.9 26 | ??? Cu 1.9 27 | ??? Zn 1.6 28 | ??? Ga 1.6 29 | ??? Ge 1.8 30 | ??? As 2.0 31 | ??? Se 2.4 32 | ??? Br 2.8 33 | ??? Rb 0.8 34 | ??? Sr 1.0 35 | ??? Y 1.2 36 | ??? Zr 1.4 37 | ??? Nb 1.6 38 | ??? Mo 1.8 39 | ??? Tc 1.9 40 | ??? Ru 2.2 41 | ??? Rh 2.2 42 | ??? Pd 2.2 43 | ??? Ag 1.9 44 | ??? Cd 1.7 45 | ??? In 1.7 46 | ??? Sn 1.8 47 | ??? Sb 1.9 48 | ??? Te 2.1 49 | ??? I 2.5 50 | ??? Cs 0.7 51 | ??? Ba 0.9 52 | ??? Hf 1.3 53 | ??? Ta 1.5 54 | ??? W 1.7 55 | ??? Re 1.9 56 | ??? Os 2.2 57 | ??? Ir 2.2 58 | ??? Pt 2.2 59 | ??? Au 2.4 60 | ??? Hg 1.9 61 | ??? Tl 1.8 62 | ??? Pb 1.9 63 | ??? Bi 1.9 64 | ??? Po 2.0 65 | ??? At 2.2 66 | ??? Fr 0.7 67 | ??? Ra 0.9 68 | ??? Ac 1.1 69 | ??? Th 1.3 70 | ??? Pa 1.4 71 | ??? U 1.4 72 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/ffamber03-c.tdb: -------------------------------------------------------------------------------- 1 | [ none ] 2 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/ffamber03-n.tdb: -------------------------------------------------------------------------------- 1 | [ none ] 2 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/forcefield.doc: -------------------------------------------------------------------------------- 1 | AMBER03 : Neutral GFP 2 | 3 | ******************************************************************** 4 | * The original ffamber ports were written by Eric J. Sorin, * 5 | * CSU Long Beach, Dept. of Chem & Biochem, and have now been * 6 | * integrated with the standard gromacs distribution. * 7 | * (Please don't blame Eric for errors we might have introduced.) * 8 | * For the implementation/validation, please read/cite: * 9 | * Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. * 10 | * For related material and updates, please consult * 11 | * http://chemistry.csulb.edu/ffamber/ * 12 | ******************************************************************** 13 | 14 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/forcefield.itp: -------------------------------------------------------------------------------- 1 | ; ######################################################################## 2 | ; # # 3 | ; # ffamber ports for GROMACS 3.3.1 - August 2007 # 4 | ; # Eric J. Sorin - CSU Long Beach, Dept. of Chem & Biochem # 5 | ; # With significant contributions from Sanghyun Park and Jory Z. Ruscio # 6 | ; # Please cite: Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. # 7 | ; # For additional information, tools, and updates # 8 | ; # please consult http://chemistry.csulb.edu/ffamber/ # 9 | ; # # 10 | ; ######################################################################## 11 | 12 | #define _FF_AMBER 13 | #define _FF_AMBER99 14 | 15 | [ defaults ] 16 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 17 | 1 2 yes 0.5 0.8333 18 | 19 | #include "ffamber03nb.itp" 20 | #include "ffamber03bon.itp" 21 | 22 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/gurgle.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioexcel/gromacs-2022-cp2k-tutorial/de2d4e83c20cb350ea3b962ef1d5d017e2c95d33/egfp/amber03_gfp.ff/gurgle.dat -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/ha-shift.dat: -------------------------------------------------------------------------------- 1 | 18 18 2 | 0.58 0.62 0.63 0.59 0.51 0.40 0.28 0.18 0.10 0.05 0.00 -0.13 -0.19 -0.13 0.07 0.29 0.41 0.51 3 | 0.62 0.65 0.65 0.61 0.52 0.40 0.27 0.15 0.07 0.01 -0.01 -0.02 -0.02 0.05 0.18 0.33 0.46 0.55 4 | 0.62 0.65 0.65 0.61 0.52 0.39 0.25 0.13 0.03 -0.03 -0.08 -0.13 -0.11 -0.02 0.11 0.30 0.46 0.56 5 | 0.59 0.63 0.63 0.59 0.51 0.38 0.24 0.11 0.00 -0.09 -0.24 -0.38 -0.33 -0.24 -0.09 0.17 0.40 0.52 6 | 0.54 0.58 0.59 0.56 0.48 0.36 0.22 0.09 -0.03 -0.22 -0.52 -0.61 -0.55 -0.49 -0.41 -0.14 0.25 0.45 7 | 0.46 0.51 0.52 0.49 0.41 0.31 0.19 0.06 -0.11 -0.45 -0.70 -0.69 -0.65 -0.64 -0.64 -0.55 -0.04 0.32 8 | 0.35 0.39 0.38 0.34 0.26 0.17 0.08 -0.03 -0.23 -0.59 -0.70 -0.67 -0.66 -0.67 -0.72 -0.78 -0.41 0.15 9 | 0.24 0.27 0.22 0.14 0.05 -0.03 -0.11 -0.17 -0.28 -0.53 -0.64 -0.64 -0.65 -0.67 -0.72 -0.82 -0.61 0.01 10 | 0.18 0.19 0.12 0.02 -0.08 -0.16 -0.22 -0.27 -0.31 -0.42 -0.58 -0.62 -0.64 -0.66 -0.70 -0.75 -0.54 -0.01 11 | 0.14 0.13 0.06 -0.06 -0.16 -0.24 -0.29 -0.32 -0.35 -0.38 -0.51 -0.61 -0.63 -0.65 -0.66 -0.65 -0.34 0.04 12 | 0.11 0.09 -0.01 -0.13 -0.22 -0.29 -0.33 -0.35 -0.37 -0.39 -0.45 -0.59 -0.62 -0.61 -0.60 -0.52 -0.16 0.06 13 | 0.08 0.05 -0.05 -0.18 -0.26 -0.32 -0.35 -0.37 -0.39 -0.40 -0.43 -0.54 -0.57 -0.55 -0.51 -0.39 -0.06 0.06 14 | 0.08 0.04 -0.07 -0.20 -0.28 -0.33 -0.37 -0.39 -0.40 -0.41 -0.43 -0.49 -0.49 -0.45 -0.42 -0.30 -0.01 0.07 15 | 0.11 0.07 -0.04 -0.18 -0.28 -0.33 -0.37 -0.39 -0.40 -0.41 -0.43 -0.47 -0.44 -0.39 -0.35 -0.25 0.03 0.11 16 | 0.17 0.15 0.07 -0.07 -0.21 -0.30 -0.35 -0.38 -0.39 -0.40 -0.42 -0.45 -0.43 -0.38 -0.34 -0.23 0.06 0.15 17 | 0.28 0.32 0.32 0.23 0.08 -0.08 -0.20 -0.28 -0.32 -0.35 -0.40 -0.43 -0.41 -0.38 -0.35 -0.18 0.13 0.22 18 | 0.40 0.47 0.50 0.47 0.39 0.28 0.17 0.07 -0.02 -0.16 -0.33 -0.37 -0.37 -0.35 -0.30 -0.01 0.24 0.33 19 | 0.51 0.57 0.58 0.56 0.48 0.38 0.28 0.19 0.11 0.03 -0.15 -0.29 -0.31 -0.29 -0.15 0.18 0.34 0.43 20 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/highway.dat: -------------------------------------------------------------------------------- 1 | 2 100 0.01 2 500 2 | 8 3 | 5 8 9 10 1 Red Yellow 4 | 12 6 10 10 2 Yellow Green 5 | 23 7 14 10 1 Blue Yellow 6 | 34 9 11 10 2 Green Brown 7 | 45 8 16 10 1 Red Blue 8 | 52 6 10 10 2 Grey Green 9 | 63 7 14 10 1 White Yellow 10 | 74 9 11 10 2 Green LightGoldenRod 11 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/ions.itp: -------------------------------------------------------------------------------- 1 | #ifndef _MYIONS 2 | #define _MYIONS 3 | 4 | ; *** Parameters for Amber Ions *** 5 | ; *** Maik Goette 11/05 *** 6 | 7 | ;#include "waterionsnb.itp" 8 | 9 | [ moleculetype ] 10 | ; molname nrexcl 11 | NA 1 12 | 13 | [ atoms ] 14 | ; id at type res nr residu name at name cg nr charge mass 15 | 1 amber99_31 1 NA NA 1 1.00 22.99000 16 | 17 | [ moleculetype ] 18 | ; molname nrexcl 19 | CL 1 20 | 21 | [ atoms ] 22 | ; id at type res nr residu name at name cg nr charge mass 23 | 1 amber99_30 1 CL CL 1 -1.00 35.45000 24 | 25 | [ moleculetype ] 26 | ; molname nrexcl 27 | NNA 1 28 | [ atoms ] 29 | ; id at type res nr residu name at name cg nr charge mass 30 | 1 amber99_31 1 NNA NA 1 1 22.99000 amber99_31 0.90 22.99 31 | 32 | #endif 33 | 34 | 35 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/links.dat: -------------------------------------------------------------------------------- 1 | dat 2 | dlg 3 | do_dssp 4 | edi 5 | editconf 6 | edo 7 | edr 8 | ene 9 | eneconv 10 | eps 11 | g87 12 | g96 13 | g_anaeig 14 | g_analyze 15 | g_angle 16 | g_bond 17 | g_bundle 18 | g_chi 19 | g_cluster 20 | g_confrms 21 | g_coord 22 | g_covar 23 | g_density 24 | g_dielectric 25 | g_dih 26 | g_dipoles 27 | g_disre 28 | g_dist 29 | g_dyndom 30 | g_enemat 31 | g_energy 32 | g_filter 33 | g_gyrate 34 | g_h2order 35 | g_hbond 36 | g_helix 37 | g_mdmat 38 | g_mindist 39 | g_morph 40 | g_msd 41 | g_nmeig 42 | g_nmens 43 | g_order 44 | g_potential 45 | g_rama 46 | g_rdf 47 | g_rms 48 | g_rmsdist 49 | g_rmsf 50 | g_rotacf 51 | g_saltbr 52 | g_sas 53 | g_sgangle 54 | g_sorient 55 | g_tcaf 56 | g_traj 57 | g_velacc 58 | genbox 59 | genconf 60 | gendr 61 | genion 62 | genpr 63 | gmxcheck 64 | gmxdump 65 | gro 66 | grompp 67 | hdb 68 | highway 69 | itp 70 | m2p 71 | make_ndx 72 | mdp 73 | mdrun 74 | mk_angndx 75 | mtx 76 | ndx 77 | ngmx 78 | pdb 79 | pdb2gmx 80 | protonate 81 | rtp 82 | tex 83 | top 84 | tpa 85 | tpb 86 | tpbconv 87 | tpr 88 | trj 89 | trjcat 90 | trjconv 91 | trjorder 92 | trr 93 | wheel 94 | x2top 95 | xpm 96 | xpm2ps 97 | xrama 98 | xtc 99 | xvg 100 | map 101 | log 102 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/phbres.dat: -------------------------------------------------------------------------------- 1 | 19 2 | ACE 3 | ALA 4 | CYS 5 | CYS1 6 | CYS2 7 | CYSH 8 | HYP 9 | ILE 10 | LEU 11 | MET 12 | PHE 13 | PHEH 14 | PRO 15 | TRP 16 | TRPH 17 | TYR 18 | TYRH 19 | VAL 20 | AIB 21 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/random.dat: -------------------------------------------------------------------------------- 1 | GLY H 8.39 2 | GLY 1HA 3.97 3 | GLY 2HA 3.97 4 | GLY HA1 3.97 5 | GLY HA2 3.97 6 | ALA H 8.25 7 | ALA HA 4.35 8 | ALA 1HB 1.40 9 | ALA HB1 1.40 10 | VAL H 8.44 11 | VAL HA 4.18 12 | VAL HB 2.13 13 | VAL 1HG1 0.96 14 | VAL 1HG2 0.96 15 | VAL HG11 0.96 16 | VAL HG21 0.96 17 | ILE H 8.20 18 | ILE HA 4.22 19 | ILE HB 1.89 20 | ILE 1HG2 0.94 21 | ILE HG21 0.94 22 | ILE 1HG1 1.30 23 | ILE HG11 1.30 24 | ILE 1HD1 0.89 25 | ILE HD11 0.89 26 | LEU H 8.42 27 | LEU HA 4.39 28 | LEU 1HB 1.65 29 | LEU 2HB 1.65 30 | LEU HB1 1.65 31 | LEU HB2 1.65 32 | LEU HG 1.65 33 | LEU 1HD1 0.92 34 | LEU HD11 0.92 35 | LEU 1HD2 0.92 36 | LEU HD21 0.92 37 | SER H 8.38 38 | SER HA 4.50 39 | SER 1HB 3.89 40 | SER 2HB 3.89 41 | SER HB1 3.89 42 | SER HB2 3.89 43 | THR H 8.24 44 | THR HA 4.35 45 | THR HB 4.22 46 | THR 1HG2 1.23 47 | THR HG21 1.23 48 | ASP H 8.41 49 | ASP HA 4.77 50 | ASP 1HB 2.80 51 | ASP 2HB 2.80 52 | ASP HB1 2.80 53 | ASP HB2 2.80 54 | GLU H 8.37 55 | GLU HA 4.30 56 | GLU 1HB 2.03 57 | GLU 2HB 2.03 58 | GLU HB1 2.03 59 | GLU HB2 2.03 60 | GLU 1HG 2.30 61 | GLU 2HG 2.30 62 | GLU HG1 2.30 63 | GLU HG2 2.30 64 | LYS H 8.41 65 | LYS HA 4.36 66 | LYS 1HB 1.81 67 | LYS 2HB 1.81 68 | LYS HB1 1.81 69 | LYS HB2 1.81 70 | LYS 1HG 1.47 71 | LYS 2HG 1.47 72 | LYS HG1 1.47 73 | LYS HG2 1.47 74 | LYS 1HD 1.71 75 | LYS 2HD 1.71 76 | LYS HD1 1.71 77 | LYS HD2 1.71 78 | LYS 1HE 3.02 79 | LYS 2HE 3.02 80 | LYS HE1 3.02 81 | LYS HE2 3.02 82 | ARG H 8.27 83 | ARG HA 4.40 84 | ARG 1HB 1.85 85 | ARG 2HB 1.85 86 | ARG HB1 1.85 87 | ARG HB2 1.85 88 | ARG 1HG 1.72 89 | ARG 2HG 1.72 90 | ARG HG1 1.72 91 | ARG HG2 1.72 92 | ARG 1HD 3.31 93 | ARG 2HD 3.31 94 | ARG HD1 3.31 95 | ARG HD2 3.31 96 | ASN H 8.75 97 | ASN HA 4.76 98 | ASN 1HB 2.80 99 | ASN 2HB 2.80 100 | ASN HB1 2.80 101 | ASN HB2 2.80 102 | GLN H 8.41 103 | GLN HA 4.37 104 | GLN 1HB 2.08 105 | GLN 2HB 2.08 106 | GLN HB1 2.08 107 | GLN HB2 2.08 108 | GLN 1HG 2.38 109 | GLN 2HG 2.38 110 | GLN HG1 2.38 111 | GLN HG2 2.38 112 | MET H 8.42 113 | MET HA 4.51 114 | MET 1HB 2.08 115 | MET 2HB 2.08 116 | MET HB1 2.08 117 | MET HB2 2.08 118 | MET 1HG 2.63 119 | MET 2HG 2.63 120 | MET HG1 2.63 121 | MET HG2 2.63 122 | MET 1HE 2.13 123 | MET HE1 2.13 124 | CYS H 8.31 125 | CYS HA 4.69 126 | CYS 1HB 3.16 127 | CYS 2HB 3.16 128 | CYS HB1 3.16 129 | CYS HB2 3.16 130 | TRP H 8.09 131 | TRP HA 4.70 132 | TRP 1HB 3.26 133 | TRP 2HB 3.26 134 | TRP HB1 3.26 135 | TRP HB2 3.26 136 | TRP HE1 9.99 137 | TRP HD1 7.24 138 | TRP HE3 7.65 139 | TRP HZ3 7.17 140 | TRP HH2 7.24 141 | TRP HZ2 7.50 142 | PHE H 8.23 143 | PHE HA 4.66 144 | PHE 1HB 3.11 145 | PHE 2HB 3.11 146 | PHE HB1 3.11 147 | PHE HB2 3.11 148 | PHE HD1 7.34 149 | PHE HE1 7.34 150 | PHE HZ 7.34 151 | TYR H 8.18 152 | TYR HA 4.60 153 | TYR 1HB 3.02 154 | TYR 2HB 3.02 155 | TYR HB1 3.02 156 | TYR HB2 3.02 157 | TYR HD1 7.15 158 | TYR HE1 6.86 159 | HIS H 8.42 160 | HIS HA 4.63 161 | HIS 1HB 3.23 162 | HIS 2HB 3.23 163 | HIS HB1 3.23 164 | HIS HB2 3.23 165 | HIS HE1 8.12 166 | HIS HD1 7.14 167 | PRO HA 4.47 168 | PRO 1HB 2.16 169 | PRO 2HB 2.16 170 | PRO HB1 2.16 171 | PRO HB2 2.16 172 | PRO 1HG 2.03 173 | PRO 2HG 2.03 174 | PRO HG1 2.03 175 | PRO HG2 2.03 176 | PRO 1HD 3.65 177 | PRO 2HD 3.65 178 | PRO HD1 3.65 179 | PRO HD2 3.65 180 | 181 | 182 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/specbond.dat: -------------------------------------------------------------------------------- 1 | 12 2 | CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 3 | CYS SG 1 HEME FE 2 0.25 CYS2 HEME 4 | CYS SG 1 HEME CAB 1 0.18 CYS2 HEME 5 | CYS SG 1 HEME CAC 1 0.18 CYS2 HEME 6 | HID NE2 1 HEME FE 1 0.21 HID HEME 7 | MET SD 1 HEME FE 1 0.23 MET HEME 8 | CYM SG 1 CYM SG 1 0.25 CYS2 CYS2 9 | HID NE2 1 BCL MG 1 0.25 HID BCL 10 | HID NE2 1 FE FE 1 0.23 HID FE 11 | GLU OE1 1 FE FE 1 0.25 GLU FE 12 | GLU OE2 1 FE FE 1 0.25 GLU FE 13 | CYS2 SG 1 PCB CBC 1 0.16 CYS2 PCB 14 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/surface.dat: -------------------------------------------------------------------------------- 1 | 34 2 | ALA 112 3 | ARG 261 4 | ARGN 261 5 | ASN 172 6 | ASP 173 7 | ASPH 173 8 | CYS 141 9 | CYS2 141 10 | CYSH 141 11 | GLN 207 12 | GLU 206 13 | GLUH 206 14 | GLY 86 15 | HIS 195 16 | HIS1 195 17 | HISA 195 18 | HISB 195 19 | HISH 195 20 | ILE 184 21 | LEU 186 22 | LYS 221 23 | LYSH 221 24 | MET 186 25 | PHE 216 26 | PRO 135 27 | SER 130 28 | THR 155 29 | TRP 258 30 | TYR 237 31 | VAL 156 32 | ASN1 172 33 | PHEH 216 34 | TRPH 258 35 | TYRH 237 36 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/tip3p.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 1 4 | 5 | [ atoms ] 6 | #ifdef _FF_AMBER94 7 | ; nr type resnr residue atom cgnr charge mass 8 | 1 amber94_42 1 SOL OW 1 -0.834 16.00000 9 | 2 amber94_27 1 SOL HW1 1 0.417 1.00800 10 | 3 amber94_27 1 SOL HW2 1 0.417 1.00800 11 | #endif 12 | #ifdef _FF_AMBER99 13 | 1 amber99_42 1 SOL OW 1 -0.834 16.00000 14 | 2 amber99_27 1 SOL HW1 1 0.417 1.00800 15 | 3 amber99_27 1 SOL HW2 1 0.417 1.00800 16 | #endif 17 | #ifndef FLEXIBLE 18 | [ settles ] 19 | ; OW funct doh dhh 20 | 1 1 0.09572 0.15139 21 | #else 22 | [ bonds ] 23 | 1 2 1 24 | 1 3 1 25 | [ angles ] 26 | 2 1 3 1 27 | #endif 28 | 29 | [ exclusions ] 30 | 1 2 3 31 | 2 1 3 32 | 3 1 2 33 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/tip4p.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 1 4 | 5 | [ atoms ] 6 | ; at type res nr res name at name cg nr charge mass 7 | #ifdef _FF_AMBER94 8 | 1 amber94_63 1 SOL OW 1 0 16.00000 9 | 2 amber94_62 1 SOL HW2 1 0.52 1.00800 10 | 3 amber94_62 1 SOL HW3 1 0.52 1.00800 11 | 4 MW 1 SOL MW4 1 -1.04 0.00000 12 | #endif 13 | #ifdef _FF_AMBER99 14 | 1 amber99_63 1 SOL OW 1 0 16.00000 15 | 2 amber99_62 1 SOL HW2 1 0.52 1.00800 16 | 3 amber99_62 1 SOL HW3 1 0.52 1.00800 17 | 4 MW 1 SOL MW4 1 -1.04 0.00000 18 | #endif 19 | 20 | [ settles ] 21 | ; i funct doh dhh 22 | 1 1 0.09572 0.15139 23 | 24 | [ dummies3 ] 25 | ; Dummy from funct a b 26 | 4 1 2 3 1 0.128012065 0.128012065 27 | 28 | [ exclusions ] 29 | 1 2 3 4 30 | 2 1 3 4 31 | 3 1 2 4 32 | 4 1 2 3 33 | 34 | 35 | ; The position of the dummy is computed as follows: 36 | ; 37 | ; O 38 | ; 39 | ; D 40 | ; 41 | ; H H 42 | ; 43 | ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ] 44 | ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ] 45 | ; 46 | ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1) 47 | 48 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/vdwradii.dat: -------------------------------------------------------------------------------- 1 | ; Very approximate VanderWaals radii 2 | ; only used for drawing atoms as balls or for calculating atomic overlap. 3 | ; longest matches are used 4 | ; '???' or '*' matches any residue name 5 | ; 'AAA' matches any protein residue name 6 | ??? C 0.15 7 | ??? F 0.12 8 | ??? H 0.04 9 | ??? N 0.110 10 | ??? O 0.105 11 | ??? S 0.16 12 | ; Water charge sites 13 | SOL MW 0 14 | SOL LP 0 15 | ; Masses for vsite construction 16 | GLY MN1 0 17 | GLY MN2 0 18 | ALA MCB1 0 19 | ALA MCB2 0 20 | VAL MCG1 0 21 | VAL MCG2 0 22 | ILE MCG1 0 23 | ILE MCG2 0 24 | ILE MCD1 0 25 | ILE MCD2 0 26 | LEU MCD1 0 27 | LEU MCD2 0 28 | MET MCE1 0 29 | MET MCE2 0 30 | TRP MTRP1 0 31 | TRP MTRP2 0 32 | THR MCG1 0 33 | THR MCG2 0 34 | LYSH MNZ1 0 35 | LYSH MNZ2 0 36 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/watermodels.dat: -------------------------------------------------------------------------------- 1 | tip3p TIP3P TIP 3-point, recommended 2 | tip4p TIP4P TIP 4-point 3 | spc SPC simple point charge 4 | -------------------------------------------------------------------------------- /egfp/amber03_gfp.ff/xlateat.dat: -------------------------------------------------------------------------------- 1 | 14 2 | ILE CD1 CD 3 | ILE HD11 HD1 4 | ILE HD12 HD2 5 | ILE HD13 HD3 6 | HOH O OW 7 | HOH OW1 OW 8 | HO4 O OW 9 | HO4 OW1 OW 10 | HO5 O OW 11 | HO5 OW1 OW 12 | HEME N_A NA 13 | HEME N_B NB 14 | HEME N_C NC 15 | HEME N_D ND -------------------------------------------------------------------------------- /egfp/conv.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import sys 4 | import numpy as np 5 | import math 6 | 7 | if __name__ == '__main__': 8 | if (len(sys.argv) != 5): 9 | print( './conv.py excitations sigma(eV) min(eV) max(eV)', file=sys.stderr) 10 | sys.exit(-1) 11 | 12 | # load data 13 | exc = np.loadtxt(sys.argv[1]) 14 | sigma = float(sys.argv[2]) 15 | mine = float(sys.argv[3]) 16 | maxe = float(sys.argv[4]) 17 | 18 | #convolved spectra 19 | spec = np.zeros((math.ceil((maxe-mine)/0.01),2)) 20 | i = 0 21 | for pt in np.arange(mine, maxe, 0.01): 22 | v = 0.0 23 | for tr in range (exc.shape[0]): 24 | v += exc[tr,1]* math.exp(-(pt-exc[tr,0])**2 / sigma**2) 25 | spec[i,0] = pt 26 | spec[i,1] = v 27 | i = i+1 28 | np.savetxt("spec.xvg", spec, delimiter='\t') 29 | -------------------------------------------------------------------------------- /egfp/em.mdp: -------------------------------------------------------------------------------- 1 | ; em.mdp - used as input into grompp to generate egfp-em.tpr 2 | integrator = steep ; Algorithm (steep = steepest descent minimization) 3 | emtol = 10.0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm 4 | emstep = 0.01 ; Energy step size 5 | nsteps = 1000 ; Maximum number of (minimization) steps to perform 6 | 7 | ; Set output frequency to each step 8 | nstxout = 1000 ; Coordinates to trr 9 | nstlog = 1000 ; Energies to md.log 10 | nstcalcenergy = 100 ; Energies to ener.edr 11 | nstenergy = 100 ; Energies to ener.edr 12 | 13 | ; Set cut-offs 14 | rlist = 1.2 15 | coulombtype = PME 16 | coulomb-modifier = Potential-shift-Verlet 17 | rcoulomb-switch = 1.0 18 | rcoulomb = 1.2 19 | vdwtype = Cut-off 20 | vdw-modifier = Force-switch 21 | rvdw-switch = 1.0 22 | rvdw = 1.2 23 | 24 | -------------------------------------------------------------------------------- /egfp/md-mm-nvt.mdp: -------------------------------------------------------------------------------- 1 | ; md-mm-nvt.mdp - used as input into grompp to generate egfp-mm-nvt.tpr 2 | integrator = md ; MD using leap-frog integrator 3 | dt = 0.001 ; 1fs time-step 4 | nsteps = 100000; 100 ps simulation 5 | 6 | ; Set output frequency to each step 7 | nstxout = 10000 ; Coordinates to trr 8 | nstvout = 10000 ; Coordinates to trr 9 | nstlog = 10000 ; Energies to md.log 10 | nstcalcenergy = 1000 ; Energies to ener.edr 11 | nstenergy = 1000 ; Energies to ener.edr 12 | 13 | ; Set cut-offs 14 | rlist = 1.2 15 | coulombtype = PME 16 | coulomb-modifier = Potential-shift-Verlet 17 | rcoulomb-switch = 1.0 18 | rcoulomb = 1.2 19 | vdwtype = Cut-off 20 | vdw-modifier = Force-switch 21 | rvdw-switch = 1.0 22 | rvdw = 1.2 23 | 24 | ;Temperature coupling options 25 | tcoupl = v-rescale 26 | nsttcouple = 10 27 | tc-grps = System 28 | tau-t = 0.1 29 | ref-t = 300 30 | 31 | ; GENERATE VELOCITIES FOR STARTUP RUN 32 | gen-vel = yes 33 | gen-temp = 300 34 | gen-seed = -1 35 | 36 | ; CP2K QMMM parameters 37 | qmmm-cp2k-active = false ; This is MM equilibration! 38 | -------------------------------------------------------------------------------- /egfp/md-qmmm-nvt.mdp: -------------------------------------------------------------------------------- 1 | ; md-qmmm-nvt.mdp - used as input into grompp to generate egfp-qmmm-nvt.tpr 2 | integrator = md ; MD using leap-frog integrator 3 | dt = 0.001 ; 1fs time-step 4 | nsteps = 100 ; 100 ps simulation 5 | 6 | ; Set output frequency to each step 7 | nstxout = 10 ; Coordinates to trr 8 | nstvout = 10 ; Coordinates to trr 9 | nstlog = 1 ; Energies to md.log 10 | nstcalcenergy = 1 ; Energies to ener.edr 11 | nstenergy = 1 ; Energies to ener.edr 12 | 13 | ; Set cut-offs 14 | rlist = 1.2 15 | coulombtype = PME 16 | coulomb-modifier = Potential-shift-Verlet 17 | rcoulomb-switch = 1.0 18 | rcoulomb = 1.2 19 | vdwtype = Cut-off 20 | vdw-modifier = Force-switch 21 | rvdw-switch = 1.0 22 | rvdw = 1.2 23 | 24 | ;Temperature coupling options 25 | tcoupl = v-rescale 26 | nsttcouple = 10 27 | tc-grps = System 28 | tau-t = 0.1 29 | ref-t = 300 30 | 31 | ; CP2K QMMM parameters 32 | qmmm-cp2k-active = true ; Activate QMMM MdModule 33 | qmmm-cp2k-qmgroup = QMatoms; Index group of QM atoms 34 | qmmm-cp2k-qmmethod = PBE ; Method to use 35 | qmmm-cp2k-qmcharge = -1 ; Charge of QM system 36 | qmmm-cp2k-qmmultiplicity = 1 ; Multiplicity of QM system 37 | -------------------------------------------------------------------------------- /egfp/md-qmmm-spec.mdp: -------------------------------------------------------------------------------- 1 | ; md-qmmm-spec.mdp - used as input into grompp to generate egfp-qmmm-spec.tpr 2 | integrator = md ; MD using leap-frog integrator 3 | dt = 0.001 ; 1fs time-step 4 | nsteps = 100 ; 100 ps simulation 5 | 6 | ; Set output frequency to each step 7 | nstxout = 10 ; Coordinates to trr 8 | nstvout = 10 ; Coordinates to trr 9 | nstlog = 1 ; Energies to md.log 10 | nstcalcenergy = 1 ; Energies to ener.edr 11 | nstenergy = 1 ; Energies to ener.edr 12 | 13 | ; Set cut-offs 14 | rlist = 1.2 15 | coulombtype = PME 16 | coulomb-modifier = Potential-shift-Verlet 17 | rcoulomb-switch = 1.0 18 | rcoulomb = 1.2 19 | vdwtype = Cut-off 20 | vdw-modifier = Force-switch 21 | rvdw-switch = 1.0 22 | rvdw = 1.2 23 | 24 | ;Temperature coupling options 25 | tcoupl = v-rescale 26 | nsttcouple = 10 27 | tc-grps = System 28 | tau-t = 0.1 29 | ref-t = 300 30 | 31 | ; CP2K QMMM parameters 32 | qmmm-cp2k-active = true ; Activate QMMM MdModule 33 | qmmm-cp2k-qmgroup = QMatoms; Index group of QM atoms 34 | qmmm-cp2k-qmmethod = INPUT ; Method to use 35 | -------------------------------------------------------------------------------- /egfp/run-em.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J egfp-em 3 | #SBATCH --time=00:20:00 4 | #SBATCH --partition=test 5 | 6 | #SBATCH --nodes=1 7 | #SBATCH --tasks-per-node=32 8 | #SBATCH --cpus-per-task=4 9 | 10 | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK 11 | export OMP_PLACES=cores 12 | 13 | srun gmx mdrun -s egfp-em.tpr -deffnm egfp-em 14 | -------------------------------------------------------------------------------- /egfp/run-mm-nvt.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J egfp-em 3 | #SBATCH --time=00:20:00 4 | #SBATCH --partition=test 5 | 6 | #SBATCH --nodes=1 7 | #SBATCH --tasks-per-node=32 8 | #SBATCH --cpus-per-task=4 9 | 10 | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK 11 | export OMP_PLACES=cores 12 | 13 | srun gmx mdrun -s egfp-mm-nvt.tpr -deffnm egfp-mm-nvt 14 | -------------------------------------------------------------------------------- /egfp/run-qmmm-nvt.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J egfp-em 3 | #SBATCH --time=00:20:00 4 | #SBATCH --partition=test 5 | 6 | #SBATCH --nodes=1 7 | #SBATCH --tasks-per-node=32 8 | #SBATCH --cpus-per-task=4 9 | 10 | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK 11 | export OMP_PLACES=cores 12 | 13 | srun gmx mdrun -s egfp-qmmm-nvt.tpr -deffnm egfp-qmmm-nvt 14 | -------------------------------------------------------------------------------- /egfp/run-qmmm-spec.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J egfp-em 3 | #SBATCH --time=00:20:00 4 | #SBATCH --partition=test 5 | 6 | #SBATCH --nodes=1 7 | #SBATCH --tasks-per-node=32 8 | #SBATCH --cpus-per-task=4 9 | 10 | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK 11 | export OMP_PLACES=cores 12 | 13 | srun gmx mdrun -s egfp-qmmm-spec.tpr -deffnm egfp-qmmm-spec 14 | -------------------------------------------------------------------------------- /egfp/xlateat.dat: -------------------------------------------------------------------------------- 1 | 14 2 | ILE CD1 CD 3 | ILE HD11 HD1 4 | ILE HD12 HD2 5 | ILE HD13 HD3 6 | HOH O OW 7 | HOH OW1 OW 8 | HO4 O OW 9 | HO4 OW1 OW 10 | HO5 O OW 11 | HO5 OW1 OW 12 | HEME N_A NA 13 | HEME N_B NB 14 | HEME N_C NC 15 | HEME N_D ND -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/forcefield.itp: -------------------------------------------------------------------------------- 1 | ; This force field generated by charmm2gmx.py from 2 | ; multiple charmm parameter files 3 | ; and multiple charmm topology files 4 | #define _FF_CHARMM 5 | 6 | ; This GROMACS version was created from: 7 | ; CHARMM parameters: multiple files 8 | ; CHARMM topology: multiple files 9 | ; Please see forcefield.doc for files and references 10 | [ defaults ] 11 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 12 | 1 2 yes 1.0 1.0 13 | 14 | #include "ffnonbonded.itp" 15 | #include "ffbonded.itp" 16 | #include "gb.itp" 17 | 18 | ; Allow the user to specify CHARMM36 parameters, instead 19 | ; Default behavior is to use CHARMM36m 20 | #ifdef USE_OLD_C36 21 | #include "old_c36_cmap.itp" 22 | #else 23 | #include "cmap.itp" 24 | #endif 25 | 26 | #include "nbfix.itp" 27 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/gb.itp: -------------------------------------------------------------------------------- 1 | 2 | [ implicit_genborn_params ] 3 | 4 | ; Atom type sar st pi gbr hct 5 | NH1 0.155 1 1.028 0.17063 0.79 ; N 6 | N 0.155 1 1 0.155 0.79 ; Proline backbone N 7 | NP 0.155 1 1 0.155 0.79 ; Proline backbone N for Proline N-terminus 8 | H 0.1 1 1 0.115 0.85 ; H 9 | CT1 0.180 1 1.276 0.190 0.72 ; C 10 | HB1 0.1 1 1 0.125 0.85 ; H 11 | CT3 0.200 1 0.880 0.190 0.72 ; C 12 | HA 0.1 1 1 0.125 0.85 ; H 13 | C 0.172 1 1.554 0.1875 0.72 ; C 14 | O 0.150 1 0.926 0.148 0.85 ; O 15 | CT2 0.190 1 1.045 0.190 0.72 ; C 16 | NC2 0.160 1 1.215 0.17063 0.79 ; N 17 | HC 0.1 1 1 0.115 0.85 ; H 18 | CC 0.172 1 1.554 0.1875 0.72 ; C 19 | CD 0.172 1 1.554 0.1875 0.72 ; carbonyl C (in COOH termini) 20 | NH2 0.160 1 1.215 0.17063 0.79 ; N 21 | OC 0.170 1 0.922 0.148 0.85 ; O 22 | OB 0.170 1 0.922 0.148 0.85 ; carbonyl O (in COOH termini) 23 | S 0.180 1 1.121 0.1775 0.96 ; S 24 | SM 0.180 1 1.121 0.1775 0.96 ; disulfide sulfur 25 | HS 0.1 1 1 0.125 0.85 ; H 26 | NR1 0.155 1 1.028 0.17063 0.79 ; N 27 | CPH1 0.172 1 1.554 0.1875 0.72 ; C 28 | CPH2 0.180 1 1.073 0.1875 0.72 ; C 29 | HR1 0.1 1 1 0.125 0.85 ; H 30 | HR2 0.1 1 1 0.125 0.85 ; H 31 | NR2 0.155 1 1.215 0.17063 0.79 ; N 32 | HR3 0.1 1 1 0.115 0.85 ; H 33 | NR3 0.155 1 1.215 0.17063 0.79 ; N 34 | NH3 0.160 1 1.215 0.1625 0.79 ; N 35 | HP 0.1 1 1 0.125 0.85 ; H 36 | CP3 0.190 1 1.045 0.190 0.72 ; C 37 | CP1 0.180 1 1.276 0.190 0.72 ; C 38 | CP2 0.190 1 1.045 0.190 0.72 ; C 39 | OH1 0.152 1 1.080 0.1535 0.85 ; O 40 | CY 0.172 0.012 1.554 0.1875 0.72 ; C 41 | CA 0.180 1 1.073 0.1875 0.72 ; C 42 | HP 0.1 1 1 0.125 0.85 ; H 43 | NY 0.155 1 1.028 0.17063 0.79 ; N 44 | CPT 0.172 0.012 1.554 0.1875 0.72 ; C 45 | MNH3 0 0 0 0 0 ; vsite (rigid tetrahedrical NH3 group) 46 | MNH2 0 0 0 0 0 ; vsite 47 | MCH3 0 0 0 0 0 ; vsite (rigid CH3 group) 48 | MCH3S 0 0 0 0 0 ; vsite 49 | MW 0 0 0 0 0 ; vsite 50 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/ions.itp: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ moleculetype ] ; added by Bjelkmar Jan 2010, from c32b1/toppar/stream/toppar_water_ions.str 4 | ; molname nrexcl 5 | OH 1 6 | 7 | [ atoms ] 8 | ; id at type res nr residu name at name cg nr charge 9 | 1 OC 1 OH O1 1 -1.32 10 | 2 H 1 OH H1 1 0.32 11 | 12 | [ bonds ] 13 | ;i j funct length force.c. 14 | 1 2 1 0.09700 456056 ; hydroxyl bond 15 | 16 | [ moleculetype ] 17 | ; molname nrexcl 18 | LI 1 19 | 20 | [ atoms ] 21 | ; id at type res nr residu name at name cg nr charge 22 | 1 LIT 1 LI LI 1 1 23 | 24 | [ moleculetype ] 25 | ; molname nrexcl 26 | NA 1 27 | 28 | [ atoms ] 29 | ; id at type res nr residu name at name cg nr charge 30 | 1 SOD 1 NA NA 1 1 31 | 32 | [ moleculetype ] 33 | ; molname nrexcl 34 | K 1 35 | 36 | [ atoms ] 37 | ; id at type res nr residu name at name cg nr charge 38 | 1 POT 1 K K 1 1 39 | 40 | [ moleculetype ] 41 | ; molname nrexcl 42 | CS 1 43 | 44 | [ atoms ] 45 | ; id at type res nr residu name at name cg nr charge 46 | 1 CES 1 Ces Ces 1 1 47 | 48 | [ moleculetype ] 49 | ; molname nrexcl 50 | CL 1 51 | 52 | [ atoms ] 53 | ; id at type res nr residu name at name cg nr charge 54 | 1 CLA 1 CL CL 1 -1 55 | 56 | [ moleculetype ] 57 | ; molname nrexcl 58 | CA 1 59 | 60 | [ atoms ] 61 | ; id at type res nr residu name at name cg nr charge 62 | 1 CAL 1 Cal Cal 1 2 63 | 64 | [ moleculetype ] 65 | ; molname nrexcl 66 | MG 1 67 | 68 | [ atoms ] 69 | ; id at type res nr residu name at name cg nr charge 70 | #ifdef MG_ALLNER 71 | ; Use parameters from Allner et al. (DOI: 10.1021/ct3000734) 72 | 1 MGA 1 MG MG 1 2 73 | #else 74 | ; Standard CHARMM parameters 75 | 1 MG 1 MG MG 1 2 76 | #endif 77 | 78 | [ moleculetype ] 79 | ; molname nrexcl 80 | ZN 1 81 | 82 | [ atoms ] 83 | ; id at type res nr residu name at name cg nr charge 84 | 1 ZN 1 ZN ZN 1 2 85 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/merged.arn: -------------------------------------------------------------------------------- 1 | 2 | 3 | ; atom renaming specification 4 | ; residue gromacs forcefield 5 | * H HN 6 | 7 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/merged.c.tdb: -------------------------------------------------------------------------------- 1 | 2 | [ None ] 3 | 4 | ; CHARMM CTER 5 | [ COO- ] 6 | [ replace ] 7 | C C CC 12.011 0.34 8 | O OT1 OC 15.9994 -0.67 9 | OXT OT2 OC 15.9994 -0.67 10 | [ add ] 11 | 2 8 OT C CA N 12 | OC 15.9994 -0.67 -1 13 | [ impropers ] 14 | C CA OT2 OT1 15 | 16 | ; CHARMM CNEU 17 | [ COOH ] 18 | [ replace ] 19 | C C CD 12.011 0.72 20 | O OT1 OB 15.9994 -0.55 21 | OXT OT2 OH1 15.9994 -0.61 22 | [ add ] 23 | 2 8 OT C CA N 24 | OB 15.9994 -0.55 -1 25 | 1 2 HT2 OT2 C CA 26 | H 1.008 0.44 -1 27 | [ replace ] 28 | OT2 OT2 OH1 15.9994 -0.61 29 | [ impropers ] 30 | C CA OT2 OT1 31 | 32 | ; Created by Michel Cuendet. 33 | [ CT2 ] 34 | [ replace ] 35 | C CC 12.011 0.55 36 | O O 15.9994 -0.55 37 | [ add ] 38 | 1 2 NT C CA N 39 | NH2 14.0027 -0.62 -1 40 | 2 3 HT NT C CA 41 | H 1.008 0.00 -1 42 | [ replace ] 43 | HT1 H 1.008 0.30 ; this one is trans to O 44 | HT2 H 1.008 0.32 ; this one is cis to O 45 | [ impropers ] 46 | C NT CA O 47 | C CA NT O 48 | NT C HT1 HT2 49 | NT C HT2 HT1 50 | 51 | 52 | ; added by Justin Lemkul 53 | [ 3TER ] 54 | [ replace ] 55 | O3' ON5 15.9994 -0.66 56 | C3' CN7 12.011 0.14 57 | [ add ] 58 | 1 2 H3T O3' C3' C4' 59 | HN5 1.008 0.43 -1 60 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/merged.n.tdb: -------------------------------------------------------------------------------- 1 | 2 | [ None ] 3 | 4 | [ GLY-NH3+ ] 5 | [ replace ] 6 | N N NH3 14.0070 -0.30 7 | CA CA CT2 12.011 0.13 8 | [ Add ] 9 | 3 4 H N CA C 10 | HC 1.008 0.33 -1 11 | [ delete ] 12 | HN 13 | 14 | [ NH3+ ] 15 | [ replace ] 16 | N N NH3 14.0070 -0.30 17 | CA CA CT1 12.011 0.21 18 | HA HA HB1 1.008 0.10 19 | [ Add ] 20 | 3 4 H N CA C 21 | HC 1.008 0.33 -1 22 | [ delete ] 23 | HN 24 | 25 | [ PRO-NH2+ ] 26 | [ replace ] 27 | N N NP 14.0070 -0.07 28 | CA CA CP1 12.011 0.16 29 | CD CD CP3 12.011 0.16 30 | [ add ] 31 | 2 4 HN N CA C 32 | HC 1.008 0.24 -1 33 | 34 | ; Created by Michel Cuendet 35 | [ NH2 ] 36 | [ replace ] 37 | N NH2 14.007 -0.96 38 | CA CT1 12.011 0.19 39 | HA HB1 1.008 0.09 40 | [ add ] 41 | 2 4 H N CA C 42 | H 1.008 0.34 -1 43 | [ delete ] 44 | HN 45 | 46 | ; CHARMM NGNE patch, new 47 | [ GLY-NH2 ] 48 | [ replace ] 49 | N NH2 14.007 -0.96 50 | CA CT2 12.011 0.10 51 | HA1 HB2 1.008 0.09 52 | HA2 HB2 1.008 0.09 53 | [ add ] 54 | 2 4 H N CA C 55 | H 1.008 0.34 -1 56 | [ delete ] 57 | HN 58 | 59 | ; Created by Bjelkmar 60 | [ PRO-NH ] 61 | [ replace ] 62 | N NP 14.0070 -0.40 63 | CA CP1 12.011 -0.08 64 | CD CP3 12.011 -0.10 65 | [ add ] 66 | 1 4 H N CA C 67 | HC 1.008 0.31 -1 68 | 69 | ; added by Justin Lemkul 70 | [ 5TER ] 71 | [ replace ] 72 | O5' ON5 15.9994 -0.66 73 | C5' CN8B 12.011 0.05 74 | [ add ] 75 | 1 2 H5T O5' C5' C4' 76 | HN5 1.008 0.43 -1 77 | [ delete ] 78 | P 79 | O1P 80 | O2P 81 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/merged.r2b: -------------------------------------------------------------------------------- 1 | 2 | 3 | ; rtp residue to rtp building block table 4 | ;GMX Force-field 5 | HISD HSD 6 | HIS1 HSD 7 | HISE HSE 8 | HISH HSP 9 | LYSN LSN 10 | ASPH ASPP 11 | GLUH GLUP 12 | RA ADE 13 | RG GUA 14 | RU URA 15 | RC CYT 16 | 17 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/spc.itp: -------------------------------------------------------------------------------- 1 | 2 | [ moleculetype ] 3 | ; molname nrexcl 4 | SOL 2 5 | 6 | [ atoms ] 7 | ; nr type resnr residue atom cgnr charge mass 8 | 1 OW 1 SOL OW 1 -0.82 9 | 2 HW 1 SOL HW1 1 0.41 10 | 3 HW 1 SOL HW2 1 0.41 11 | 12 | #ifndef FLEXIBLE 13 | [ settles ] 14 | ; OW funct doh dhh 15 | 1 1 0.1 0.16330 16 | 17 | [ exclusions ] 18 | 1 2 3 19 | 2 1 3 20 | 3 1 2 21 | #else 22 | [ bonds ] 23 | ; i j funct length force.c. 24 | 1 2 1 0.1 345000 0.1 345000 25 | 1 3 1 0.1 345000 0.1 345000 26 | 27 | [ angles ] 28 | ; i j k funct angle force.c. 29 | 2 1 3 1 109.47 383 109.47 383 30 | #endif 31 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/spce.itp: -------------------------------------------------------------------------------- 1 | 2 | [ moleculetype ] 3 | ; molname nrexcl 4 | SOL 2 5 | 6 | [ atoms ] 7 | ; nr type resnr residue atom cgnr charge mass 8 | 1 OW 1 SOL OW 1 -0.8476 9 | 2 HW 1 SOL HW1 1 0.4238 10 | 3 HW 1 SOL HW2 1 0.4238 11 | 12 | #ifndef FLEXIBLE 13 | [ settles ] 14 | ; OW funct doh dhh 15 | 1 1 0.1 0.16330 16 | 17 | [ exclusions ] 18 | 1 2 3 19 | 2 1 3 20 | 3 1 2 21 | #else 22 | [ bonds ] 23 | ; i j funct length force.c. 24 | 1 2 1 0.1 345000 0.1 345000 25 | 1 3 1 0.1 345000 0.1 345000 26 | 27 | [ angles ] 28 | ; i j k funct angle force.c. 29 | 2 1 3 1 109.47 383 109.47 383 30 | #endif 31 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/tip3p.itp: -------------------------------------------------------------------------------- 1 | 2 | [ moleculetype ] 3 | ; molname nrexcl 4 | SOL 2 5 | 6 | [ atoms ] 7 | ; id at type res nr residu name at name cg nr charge 8 | #ifdef _FF_CHARMM 9 | 1 OT 1 SOL OW 1 -0.834 10 | 2 HT 1 SOL HW1 1 0.417 11 | 3 HT 1 SOL HW2 1 0.417 12 | #endif 13 | 14 | 15 | #ifdef FLEXIBLE 16 | 17 | #ifdef ORIGINAL_TIP3P 18 | [ bonds ] 19 | ; i j funct length force.c. 20 | 1 2 1 0.09572 502416.0 0.09572 502416.0 21 | 1 3 1 0.09572 502416.0 0.09572 502416.0 22 | 23 | [ angles ] 24 | ; i j k funct angle force.c. 25 | 2 1 3 1 104.52 628.02 104.52 628.02 26 | 27 | #else 28 | ;CHARMM TIP3p 29 | [ bonds ] 30 | ; i j funct length force.c. 31 | 1 2 1 0.09572 376560.0 0.09572 376560.0 32 | 1 3 1 0.09572 376560.0 0.09572 376560.0 33 | 34 | [ angles ] 35 | ; i j k funct angle force.c. 36 | 2 1 3 1 104.52 460.24 104.52 460.24 37 | #endif 38 | 39 | 40 | #else 41 | [ settles ] 42 | ; i j funct length 43 | 1 1 0.09572 0.15139 44 | 45 | [ exclusions ] 46 | 1 2 3 47 | 2 1 3 48 | 3 1 2 49 | #endif 50 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/tip4p.itp: -------------------------------------------------------------------------------- 1 | 2 | ; 3 | ; Note the strange order of atoms to make it faster in gromacs. 4 | ; 5 | [ moleculetype ] 6 | ; molname nrexcl 7 | SOL 2 8 | 9 | [ atoms ] 10 | ; id at type res nr residu name at name cg nr charge 11 | 1 OWT4 1 SOL OW 1 0.0 12 | 2 HWT4 1 SOL HW1 1 0.52 13 | 3 HWT4 1 SOL HW2 1 0.52 14 | 4 MWT4 1 SOL MW 1 -1.04 15 | 16 | #ifndef FLEXIBLE 17 | [ settles ] 18 | ; OW funct doh dhh 19 | 1 1 0.09572 0.15139 20 | #else 21 | [ bonds ] 22 | ; i j funct length force.c. 23 | 1 2 1 0.09572 502416.0 0.09572 502416.0 24 | 1 3 1 0.09572 502416.0 0.09572 502416.0 25 | 26 | [ angles ] 27 | ; i j k funct angle force.c. 28 | 2 1 3 1 104.52 628.02 104.52 628.02 29 | #endif 30 | 31 | [ exclusions ] 32 | 1 2 3 4 33 | 2 1 3 4 34 | 3 1 2 4 35 | 4 1 2 3 36 | 37 | ; The position of the virtual site is computed as follows: 38 | ; 39 | ; O 40 | ; 41 | ; D 42 | ; 43 | ; H H 44 | ; 45 | ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ] 46 | ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ] 47 | 48 | ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) 49 | 50 | [ virtual_sites3 ] 51 | ; Vsite from funct a b 52 | 4 1 2 3 1 0.128012065 0.128012065 53 | 54 | -------------------------------------------------------------------------------- /nma/charmm36-mar2019.ff/watermodels.dat: -------------------------------------------------------------------------------- 1 | 2 | tip3p TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 3 | tip4p TIP4P TIP 4-point 4 | tip5p TIP5P TIP 5-point 5 | spc SPC simple point charge 6 | spce SPC/E extended simple point charge 7 | -------------------------------------------------------------------------------- /nma/em.mdp: -------------------------------------------------------------------------------- 1 | ; em.mdp - used as input into grompp to generate nma-em.tpr 2 | integrator = steep ; Algorithm (steep = steepest descent minimization) 3 | emtol = 10.0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm 4 | emstep = 0.01 ; Energy step size 5 | nsteps = 100 ; Maximum number of (minimization) steps to perform 6 | 7 | ; Set output frequency to each step 8 | nstxout = 1 ; Coordinates to trr 9 | nstlog = 1 ; Energies to md.log 10 | nstcalcenergy = 1 ; Energies to ener.edr 11 | nstenergy = 1 ; Energies to ener.edr 12 | 13 | ; Set cut-offs 14 | rlist = 0.2 ; NB-search cut-off 15 | rcoulomb = 0.2 ; Short-range electrostatic cut-off 16 | rvdw = 0.2 ; Short-range Van der Waals cut-off 17 | 18 | ; CP2K QMMM parameters 19 | qmmm-cp2k-active = true ; Activate QMMM MdModule 20 | qmmm-cp2k-qmgroup = System ; Index group of QM atoms 21 | qmmm-cp2k-qmmethod = PBE ; Method to use 22 | qmmm-cp2k-qmcharge = 0 ; Charge of QM system 23 | qmmm-cp2k-qmmultiplicity = 1 ; Multiplicity of QM system 24 | -------------------------------------------------------------------------------- /nma/md-nvt.mdp: -------------------------------------------------------------------------------- 1 | ; md-nvt.mdp - used as input into grompp to generate nma-nvt.tpr 2 | integrator = md ; MD using leap-frog integrator 3 | dt = 0.001 ; 1fs time-step 4 | nsteps = 100 ; 100 fs simulation 5 | 6 | ; Set output frequency to each step 7 | nstxout = 1 ; Coordinates to trr 8 | nstlog = 1 ; Energies to md.log 9 | nstcalcenergy = 1 ; Energies to ener.edr 10 | nstenergy = 1 ; Energies to ener.edr 11 | 12 | ; Set cut-offs 13 | rlist = 0.2 ; NB-search cut-off 14 | rcoulomb = 0.2 ; Short-range electrostatic cut-off 15 | rvdw = 0.2 ; Short-range Van der Waals cut-off 16 | 17 | ;Temperature coupling options 18 | tcoupl = v-rescale 19 | nsttcouple = 1 20 | tc-grps = System 21 | tau-t = 0.1 22 | ref-t = 300 23 | 24 | ; GENERATE VELOCITIES FOR STARTUP RUN 25 | gen-vel = yes 26 | gen-temp = 300 27 | gen-seed = -1 28 | 29 | ; CP2K QMMM parameters 30 | qmmm-cp2k-active = true ; Activate QMMM MdModule 31 | qmmm-cp2k-qmgroup = System ; Index group of QM atoms 32 | qmmm-cp2k-qmmethod = PBE ; Method to use 33 | qmmm-cp2k-qmcharge = 0 ; Charge of QM system 34 | qmmm-cp2k-qmmultiplicity = 1 ; Multiplicity of QM system 35 | -------------------------------------------------------------------------------- /nma/nma.pdb: -------------------------------------------------------------------------------- 1 | TITLE Getting the Right Output Means no Artefacts in Calculating Stuff 2 | REMARK THIS IS A SIMULATION BOX 3 | CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 1 4 | MODEL 1 5 | ATOM 1 CL NMA X 0 5.108 6.412 3.774 1.00 0.00 C 6 | ATOM 2 HL1 NMA X 0 5.678 7.332 3.774 1.00 0.00 H 7 | ATOM 3 HL2 NMA X 0 5.388 5.842 2.834 1.00 0.00 H 8 | ATOM 4 HL3 NMA X 0 4.028 6.742 3.814 1.00 0.00 H 9 | ATOM 5 C NMA X 0 5.388 5.572 4.964 1.00 0.00 C 10 | ATOM 6 O NMA X 0 6.248 5.982 5.784 1.00 0.00 O 11 | ATOM 7 N NMA X 0 4.698 4.412 5.054 1.00 0.00 N 12 | ATOM 8 HN NMA X 0 4.088 4.212 4.294 1.00 0.00 H 13 | ATOM 9 CR NMA X 0 4.808 3.542 6.184 1.00 0.00 C 14 | ATOM 10 HR1 NMA X 0 5.518 3.962 6.934 1.00 0.00 H 15 | ATOM 11 HR2 NMA X 0 5.228 2.542 5.924 1.00 0.00 H 16 | ATOM 12 HR3 NMA X 0 3.818 3.452 6.664 1.00 0.00 H 17 | TER 18 | ENDMDL 19 | -------------------------------------------------------------------------------- /nma/run-em.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J nma-em 3 | #SBATCH --time=00:10:00 4 | #SBATCH --partition=test 5 | 6 | #SBATCH --nodes=1 7 | #SBATCH --tasks-per-node=32 8 | #SBATCH --cpus-per-task=4 9 | 10 | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK 11 | export OMP_PLACES=cores 12 | 13 | srun gmx mdrun -s nma-em.tpr -------------------------------------------------------------------------------- /nma/run-nvt.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J nma-nvt 3 | #SBATCH --time=00:20:00 4 | #SBATCH --partition=test 5 | 6 | #SBATCH --nodes=1 7 | #SBATCH --tasks-per-node=32 8 | #SBATCH --cpus-per-task=4 9 | 10 | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK 11 | export OMP_PLACES=cores 12 | 13 | srun gmx mdrun -s nma-nvt.tpr -------------------------------------------------------------------------------- /nma/specbond.dat: -------------------------------------------------------------------------------- 1 | 8 2 | CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 3 | CYS SG 1 HEM FE 2 0.25 CYS2 HEME 4 | CYS SG 1 HEM CAB 1 0.18 CYS2 HEME 5 | CYS SG 1 HEM CAC 1 0.18 CYS2 HEME 6 | HIS NE2 1 HEM FE 1 0.2 HIS1 HEME 7 | MET SD 1 HEM FE 1 0.24 MET HEME 8 | CO C 1 HEME FE 1 0.19 CO HEME 9 | CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 10 | -------------------------------------------------------------------------------- /nma/vdwradii.dat: -------------------------------------------------------------------------------- 1 | ; Very approximate VanderWaals radii 2 | ; only used for drawing atoms as balls or for calculating atomic overlap. 3 | ; longest matches are used 4 | ; '???' or '*' matches any residue name 5 | ; 'AAA' matches any protein residue name 6 | ??? C 0.15 7 | ??? F 0.12 8 | ??? H 0.04 9 | ??? N 0.110 10 | ??? O 0.105 11 | ??? S 0.16 12 | ; Water charge sites 13 | SOL MW 0 14 | SOL LP 0 15 | ; Masses for vsite construction 16 | GLY MN1 0 17 | GLY MN2 0 18 | ALA MCB1 0 19 | ALA MCB2 0 20 | VAL MCG1 0 21 | VAL MCG2 0 22 | ILE MCG1 0 23 | ILE MCG2 0 24 | ILE MCD1 0 25 | ILE MCD2 0 26 | LEU MCD1 0 27 | LEU MCD2 0 28 | MET MCE1 0 29 | MET MCE2 0 30 | TRP MTRP1 0 31 | TRP MTRP2 0 32 | THR MCG1 0 33 | THR MCG2 0 34 | LYSH MNZ1 0 35 | LYSH MNZ2 0 36 | -------------------------------------------------------------------------------- /nma/xlateat.dat: -------------------------------------------------------------------------------- 1 | 26 2 | ILE CD1 CD 3 | ILE HD11 HD1 4 | ILE HD12 HD2 5 | ILE HD13 HD3 6 | HOH O OW 7 | HOH OW1 OW 8 | HO4 O OW 9 | HO4 OW1 OW 10 | HO5 O OW 11 | HO5 OW1 OW 12 | HEME N_A NA 13 | HEME N_B NB 14 | HEME N_C NC 15 | HEME N_D ND 16 | protein O1 O 17 | protein O2 OXT 18 | protein OT1 O 19 | protein OT2 OXT 20 | protein OT OXT 21 | protein O' O 22 | protein O'' OXT 23 | protein OC1 O 24 | protein OC2 OXT 25 | protein HN H 26 | protein HT1 H1 27 | protein HT2 H2 28 | protein HT3 H3 29 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/Makefile.am: -------------------------------------------------------------------------------- 1 | ## Process this file with automake to produce Makefile.in 2 | # 3 | # Don't edit - this file is generated automatically from Makefile.am 4 | # 5 | topoldir = ${pkgdatadir}/top/amber14sb.ff 6 | 7 | topol_DATA = \ 8 | aminoacids.arn aminoacids.vsd \ 9 | aminoacids.c.tdb atomtypes.atp ffnonbonded.itp \ 10 | aminoacids.hdb forcefield.doc dna.rtp dna.r2b dna.arn dna.hdb \ 11 | aminoacids.n.tdb forcefield.itp rna.rtp rna.r2b rna.arn rna.hdb \ 12 | aminoacids.r2b ffbonded.itp tip3p.itp urea.itp \ 13 | aminoacids.rtp ions.itp tip4p.itp \ 14 | tip4pew.itp tip5p.itp watermodels.dat gbsa.itp \ 15 | spc.itp spce.itp 16 | 17 | EXTRA_DIST = ${topol_DATA} 18 | 19 | CLEANFILES = *~ \\\#* 20 | 21 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/aminoacids.arn: -------------------------------------------------------------------------------- 1 | ; atom renaming specification 2 | ; residue gromacs forcefield 3 | NALA H H1 4 | NGLY H H1 5 | NSER H H1 6 | NTHR H H1 7 | NLEU H H1 8 | NILE H H1 9 | NVAL H H1 10 | NASN H H1 11 | NGLN H H1 12 | NARG H H1 13 | NHID H H1 14 | NHIE H H1 15 | NHIP H H1 16 | NTRP H H1 17 | NPHE H H1 18 | NTYR H H1 19 | NGLU H H1 20 | NASP H H1 21 | NLYS H H1 22 | NPRO H H1 23 | NCYS H H1 24 | NCYX H H1 25 | NMET H H1 26 | NGLH H H1 27 | NASP H H1 28 | ; This mapping of O->OC2 and OXT->OC1 might look a bit strange, 29 | ; but when we rebuild an oxygen it will be placed directly after C, so 30 | ; this mapping makes sure OC1 comes before OC2. The oxygens are anyway chemically 31 | ; equivalent, and if you already had their coordinates present they will be kept intact. 32 | CALA O OC2 33 | CALA OXT OC1 34 | CGLY O OC2 35 | CGLY OXT OC1 36 | CSER O OC2 37 | CSER OXT OC1 38 | CTHR O OC2 39 | CTHR OXT OC1 40 | CLEU O OC2 41 | CLEU OXT OC1 42 | CILE O OC2 43 | CILE OXT OC1 44 | CVAL O OC2 45 | CVAL OXT OC1 46 | CASN O OC2 47 | CASN OXT OC1 48 | CGLN O OC2 49 | CGLN OXT OC1 50 | CARG O OC2 51 | CARG OXT OC1 52 | CHID O OC2 53 | CHID OXT OC1 54 | CHIE O OC2 55 | CHIE OXT OC1 56 | CHIP O OC2 57 | CHIP OXT OC1 58 | CTRP O OC2 59 | CTRP OXT OC1 60 | CPHE O OC2 61 | CPHE OXT OC1 62 | CTYR O OC2 63 | CTYR OXT OC1 64 | CGLU O OC2 65 | CGLU OXT OC1 66 | CASP O OC2 67 | CASP OXT OC1 68 | CLYS O OC2 69 | CLYS OXT OC1 70 | CPRO O OC2 71 | CPRO OXT OC1 72 | CCYS O OC2 73 | CCYS OXT OC1 74 | CCYX O OC2 75 | CCYX OXT OC1 76 | CMET O OC2 77 | CMET OXT OC1 78 | CGLH O OC2 79 | CGLH OXT OC1 80 | CASH O OC2 81 | CASH OXT OC1 82 | 83 | 84 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/aminoacids.c.tdb: -------------------------------------------------------------------------------- 1 | ; empty 2 | 3 | 4 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/aminoacids.n.tdb: -------------------------------------------------------------------------------- 1 | ; empty 2 | 3 | 4 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/aminoacids.r2b: -------------------------------------------------------------------------------- 1 | ; rtp residue to rtp building block table 2 | ;GMX Force-field 3 | ; main N-ter C-ter 2-ter 4 | ALA ALA NALA CALA - 5 | ARG ARG NARG CARG - 6 | ARGN - - - - 7 | ASN ASN NASN CASN - 8 | ASP ASP NASP CASP - 9 | ASPH ASH - - - 10 | CYS CYS NCYS CCYS - 11 | CYS2 CYX NCYX CCYX - 12 | GLN GLN NGLN CGLN - 13 | QLN - - - - 14 | GLU GLU NGLU CGLU - 15 | GLY GLY NGLY CGLY - 16 | GLUH GLH - - - 17 | HISD HID NHID CHID - 18 | HISE HIE NHIE CHIE - 19 | HISH HIP NHIP CHIP - 20 | ILE ILE NILE CILE - 21 | LYSN LYN - - - 22 | LYS LYS NLYS CLYS - 23 | LEU LEU NLEU CLEU - 24 | MET MET NMET CMET - 25 | PHE PHE NPHE CPHE - 26 | PRO PRO NPRO CPRO - 27 | SER SER NSER CSER - 28 | THR THR NTHR CTHR - 29 | TRP TRP NTRP CTRP - 30 | TYR TYR NTYR CTYR - 31 | VAL VAL NVAL CVAL - 32 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/dna.arn: -------------------------------------------------------------------------------- 1 | DNA OP1 O1P 2 | DNA OP2 O2P 3 | DNA H2' H2'1 4 | DNA H2'' H2'2 5 | DNA H5' H5'1 6 | DNA H5'' H5'2 7 | DNA HO5' H5T 8 | DNA HO3' H3T 9 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/dna.r2b: -------------------------------------------------------------------------------- 1 | ; rtp residue to rtp building block table 2 | ;GMX Force-field 3 | DA DA DA5 DA3 DAN 4 | DG DG DG5 DG3 DGN 5 | DC DC DC5 DC3 DCN 6 | DT DT DT5 DT3 DTN 7 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/forcefield.doc: -------------------------------------------------------------------------------- 1 | OL15 nucleic (Zgarbova et al., J. Chem. Theory Comput. 11, 5723-36, 2015; 2 | J. Chem. Theory Comput. 7, 2886-2902, 2011) 3 | 4 | ******************************************************************** 5 | * OL15 nucleic acid package combines several dihedral * 6 | * modifications, which were added to ff99 + bsc0 force field: * 7 | * DNA: * 8 | * chiOL4 (Krepl et al. 8, 2506-2520, 2012) * 9 | * epsilon/zetaOL1 (Zgarbova et al. JCTC 9, 2339-2354, 2013) * 10 | * betaOL1 (Zgarbova et al. JCTC 11, 5723-36, 2015) * 11 | * RNA: * 12 | * chiOL3 (Zgarbova et al. JCTC 7, 2866-2902, 2011) * 13 | * see also http://ffol.upol.cz * 14 | * OL15 nucleic is combined with amber14SB protein FF implemented * 15 | * by Man Hoang Viet, vhman@ncsu.edu * 16 | ******************************************************************** 17 | 18 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/forcefield.itp: -------------------------------------------------------------------------------- 1 | ******************************************************************** 2 | * The original ffamber ports were written by Eric J. Sorin, * 3 | * CSU Long Beach, Dept. of Chem & Biochem, and have now been * 4 | * integrated with the standard gromacs distribution. * 5 | * (Please don't blame Eric for errors we might have introduced.) * 6 | * For the implementation/validation, please read/cite: * 7 | * Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. * 8 | * For related material and updates, please consult * 9 | * http://chemistry.csulb.edu/ffamber/ * 10 | ******************************************************************** 11 | 12 | #define _FF_AMBER 13 | #define _FF_AMBER12SB 14 | 15 | [ defaults ] 16 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 17 | 1 2 yes 0.5 0.8333 18 | 19 | #include "ffnonbonded.itp" 20 | #include "ffbonded.itp" 21 | #include "gbsa.itp" 22 | 23 | 24 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/gbsa.itp: -------------------------------------------------------------------------------- 1 | [ implicit_genborn_params ] 2 | 3 | ; atype sar st pi gbr hct 4 | ;Br 0.1 1 1 0.125 0.85 ; H 5 | C 0.172 1 1.554 0.1875 0.72 ; C 6 | CA 0.18 1 1.037 0.1875 0.72 ; C 7 | CB 0.172 0.012 1.554 0.1875 0.72 ; C 8 | CC 0.172 1 1.554 0.1875 0.72 ; C 9 | CN 0.172 0.012 1.554 0.1875 0.72 ; C 10 | CR 0.18 1 1.073 0.1875 0.72 ; C 11 | CT 0.18 1 1.276 0.190 0.72 ; C 12 | CV 0.18 1 1.073 0.1875 0.72 ; C 13 | CW 0.18 1 1.073 0.1875 0.72 ; C 14 | C* 0.172 0.012 1.554 0.1875 0.72 ; C 15 | H 0.1 1 1 0.115 0.85 ; H 16 | HC 0.1 1 1 0.125 0.85 ; H 17 | H1 0.1 1 1 0.125 0.85 ; H 18 | HA 0.1 1 1 0.125 0.85 ; H 19 | H4 0.1 1 1 0.115 0.85 ; H 20 | H5 0.1 1 1 0.125 0.85 ; H 21 | HO 0.1 1 1 0.105 0.85 ; H 22 | HS 0.1 1 1 0.125 0.85 ; H 23 | HP 0.1 1 1 0.125 0.85 ; H 24 | N 0.155 1 1.028 0.17063 0.79 ; N 25 | NA 0.155 1 1.028 0.17063 0.79 ; N 26 | NB 0.155 1 1.215 0.17063 0.79 ; N 27 | N2 0.16 1 1.215 0.17063 0.79 ; N 28 | N3 0.16 1 1.215 0.1625 0.79 ; N 29 | O 0.15 1 0.926 0.148 0.85 ; O 30 | OH 0.152 1 1.080 0.1535 0.85 ; O 31 | O2 0.17 1 0.922 0.148 0.85 ; O 32 | S 0.18 1 1.121 0.1775 0.96 ; S 33 | SH 0.18 1 1.121 0.1775 0.96 ; S 34 | 35 | ; masscenters for vsites do not have gbsa parameters 36 | 37 | MNH3 0 0 0 0 0 38 | MCH3 0 0 0 0 0 39 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/ions.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | IB+ 1 ; big positive ion 4 | 5 | [ atoms ] 6 | ; id at type res nr residu name at name cg nr charge 7 | 1 IB 1 IB+ IB 1 1.00000 8 | 9 | 10 | [ moleculetype ] 11 | ; molname nrexcl 12 | CA 1 13 | 14 | [ atoms ] 15 | ; id at type res nr residu name at name cg nr charge 16 | 1 C0 1 CA CA 1 2.00000 17 | 18 | 19 | [ moleculetype ] 20 | ; molname nrexcl 21 | CL 1 22 | 23 | [ atoms ] 24 | ; id at type res nr residu name at name cg nr charge 25 | 1 Cl 1 CL CL 1 -1.00000 26 | 27 | 28 | [ moleculetype ] 29 | ; molname nrexcl 30 | NA 1 31 | 32 | [ atoms ] 33 | ; id at type res nr residu name at name cg nr charge 34 | 1 Na 1 NA NA 1 1.00000 35 | 36 | 37 | [ moleculetype ] 38 | ; molname nrexcl 39 | MG 1 40 | 41 | [ atoms ] 42 | ; id at type res nr residu name at name cg nr charge 43 | 1 MG 1 MG MG 1 2.00000 44 | 45 | 46 | [ moleculetype ] 47 | ; molname nrexcl 48 | K 1 49 | 50 | [ atoms ] 51 | ; id at type res nr residu name at name cg nr charge 52 | 1 K 1 K K 1 1.00000 53 | 54 | 55 | [ moleculetype ] 56 | ; molname nrexcl 57 | RB 1 58 | 59 | [ atoms ] 60 | ; id at type res nr residu name at name cg nr charge 61 | 1 Rb 1 RB RB 1 1.00000 62 | 63 | 64 | [ moleculetype ] 65 | ; molname nrexcl 66 | CS 1 67 | 68 | [ atoms ] 69 | ; id at type res nr residu name at name cg nr charge 70 | 1 Cs 1 CS CS 1 1.00000 71 | 72 | 73 | [ moleculetype ] 74 | ; molname nrexcl 75 | LI 1 76 | 77 | [ atoms ] 78 | ; id at type res nr residu name at name cg nr charge 79 | 1 Li 1 LI LI 1 1.00000 80 | 81 | 82 | [ moleculetype ] 83 | ; molname nrexcl 84 | ZN 1 85 | 86 | [ atoms ] 87 | ; id at type res nr residu name at name cg nr charge 88 | 1 Zn 1 ZN ZN 1 2.00000 89 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/rna.arn: -------------------------------------------------------------------------------- 1 | RNA OP1 O1P 2 | RNA OP2 O2P 3 | RNA H2' H2'1 4 | RNA H2'' H2'2 5 | RNA H5' H5'1 6 | RNA H5'' H5'2 7 | RNA HO5' H5T 8 | RNA HO3' H3T 9 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/rna.r2b: -------------------------------------------------------------------------------- 1 | ; rtp residue to rtp building block table 2 | ;GMX Force-field 3 | A RA RA5 RA3 RAN 4 | U RU RU5 RU3 RUN 5 | C RC RC5 RC3 RCN 6 | G RG RG5 RG3 RGN 7 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/spc.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; id at type res nr res name at name cg nr charge mass 7 | 1 OW_spc 1 SOL OW 1 -0.82 15.99940 8 | 2 HW_spc 1 SOL HW1 1 0.41 1.00800 9 | 3 HW_spc 1 SOL HW2 1 0.41 1.00800 10 | 11 | #ifndef FLEXIBLE 12 | 13 | [ settles ] 14 | ; OW funct doh dhh 15 | 1 1 0.1 0.16330 16 | 17 | [ exclusions ] 18 | 1 2 3 19 | 2 1 3 20 | 3 1 2 21 | 22 | #else 23 | 24 | [ bonds ] 25 | ; i j funct length force.c. 26 | 1 2 1 0.1 345000 0.1 345000 27 | 1 3 1 0.1 345000 0.1 345000 28 | 29 | [ angles ] 30 | ; i j k funct angle force.c. 31 | 2 1 3 1 109.47 383 109.47 383 32 | 33 | #endif 34 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/spce.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; id at type res nr res name at name cg nr charge mass 7 | 1 OW_spc 1 SOL OW 1 -0.8476 15.99940 8 | 2 HW_spc 1 SOL HW1 1 0.4238 1.00800 9 | 3 HW_spc 1 SOL HW2 1 0.4238 1.00800 10 | 11 | #ifndef FLEXIBLE 12 | 13 | [ settles ] 14 | ; OW funct doh dhh 15 | 1 1 0.1 0.16330 16 | 17 | [ exclusions ] 18 | 1 2 3 19 | 2 1 3 20 | 3 1 2 21 | 22 | #else 23 | 24 | [ bonds ] 25 | ; i j funct length force.c. 26 | 1 2 1 0.1 345000 0.1 345000 27 | 1 3 1 0.1 345000 0.1 345000 28 | 29 | [ angles ] 30 | ; i j k funct angle force.c. 31 | 2 1 3 1 109.47 383 109.47 383 32 | 33 | #endif 34 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/tip3p.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; id at type res nr res name at name cg nr charge mass 7 | 1 OW 1 SOL OW 1 -0.834 16.00000 8 | 2 HW 1 SOL HW1 1 0.417 1.00800 9 | 3 HW 1 SOL HW2 1 0.417 1.00800 10 | 11 | #ifndef FLEXIBLE 12 | 13 | [ settles ] 14 | ; OW funct doh dhh 15 | 1 1 0.09572 0.15139 16 | 17 | [ exclusions ] 18 | 1 2 3 19 | 2 1 3 20 | 3 1 2 21 | 22 | #else 23 | 24 | [ bonds ] 25 | ; i j funct length force_constant 26 | 1 2 1 0.09572 502416.0 0.09572 502416.0 27 | 1 3 1 0.09572 502416.0 0.09572 502416.0 28 | 29 | 30 | [ angles ] 31 | ; i j k funct angle force_constant 32 | 2 1 3 1 104.52 628.02 104.52 628.02 33 | 34 | #endif 35 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/tip4p.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; id at type res nr res name at name cg nr charge mass 7 | 1 OW_tip4p 1 SOL OW 1 0 16.00000 8 | 2 HW_tip4p 1 SOL HW1 1 0.52 1.00800 9 | 3 HW_tip4p 1 SOL HW2 1 0.52 1.00800 10 | 4 MW 1 SOL MW 1 -1.04 0.00000 11 | 12 | #ifndef FLEXIBLE 13 | 14 | [ settles ] 15 | ; i funct doh dhh 16 | 1 1 0.09572 0.15139 17 | 18 | #else 19 | 20 | [ bonds ] 21 | ; i j funct length force.c. 22 | 1 2 1 0.09572 502416.0 0.09572 502416.0 23 | 1 3 1 0.09572 502416.0 0.09572 502416.0 24 | 25 | [ angles ] 26 | ; i j k funct angle force.c. 27 | 2 1 3 1 104.52 628.02 104.52 628.02 28 | 29 | #endif 30 | 31 | 32 | [ virtual_sites3 ] 33 | ; Vsite from funct a b 34 | 4 1 2 3 1 0.128012065 0.128012065 35 | 36 | 37 | [ exclusions ] 38 | 1 2 3 4 39 | 2 1 3 4 40 | 3 1 2 4 41 | 4 1 2 3 42 | 43 | 44 | ; The position of the virtual site is computed as follows: 45 | ; 46 | ; O 47 | ; 48 | ; V 49 | ; 50 | ; H H 51 | ; 52 | ; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] 53 | ; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ] 54 | ; 55 | ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) 56 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/tip4pew.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; id at type res nr res name at name cg nr charge mass 7 | 1 OW_tip4pew 1 SOL OW 1 0 16.00000 8 | 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 9 | 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 10 | 4 MW 1 SOL MW 1 -1.04844 0.00000 11 | 12 | #ifndef FLEXIBLE 13 | 14 | [ settles ] 15 | ; i funct doh dhh 16 | 1 1 0.09572 0.15139 17 | 18 | #else 19 | [ bonds ] 20 | ; i j funct length force.c. 21 | 1 2 1 0.09572 502416.0 0.09572 502416.0 22 | 1 3 1 0.09572 502416.0 0.09572 502416.0 23 | 24 | [ angles ] 25 | ; i j k funct angle force.c. 26 | 2 1 3 1 104.52 628.02 104.52 628.02 27 | 28 | #endif 29 | 30 | 31 | [ virtual_sites3 ] 32 | ; Vsite from funct a b 33 | 4 1 2 3 1 0.106676721 0.106676721 34 | 35 | 36 | [ exclusions ] 37 | 1 2 3 4 38 | 2 1 3 4 39 | 3 1 2 4 40 | 4 1 2 3 41 | 42 | 43 | ; The position of the virtual site is computed as follows: 44 | ; 45 | ; O 46 | ; 47 | ; V 48 | ; 49 | ; H H 50 | ; 51 | ; Ewald tip4p: 52 | ; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] 53 | ; 0.0125 nm / [ cos (52.26 deg) * 0.09572 nm ] 54 | ; then a = b = 0.5 * const = 0.106676721 55 | ; 56 | ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) 57 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/tip5p.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | SOL 2 4 | 5 | [ atoms ] 6 | ; id at type res nr res name at name cg nr charge mass 7 | 1 OW_tip5p 1 SOL OW 1 0 16.00000 8 | 2 HW_tip5p 1 SOL HW1 1 0.241 1.00800 9 | 3 HW_tip5p 1 SOL HW2 1 0.241 1.00800 10 | 4 MW 1 SOL LP1 1 -0.241 0.00000 11 | 5 MW 1 SOL LP2 1 -0.241 0.00000 12 | 13 | #ifndef FLEXIBLE 14 | 15 | [ settles ] 16 | ; i funct doh dhh 17 | 1 1 0.09572 0.15139 18 | 19 | #else 20 | 21 | [ bonds ] 22 | ; i j funct length force.c. 23 | 1 2 1 0.09572 502416.0 0.09572 502416.0 24 | 1 3 1 0.09572 502416.0 0.09572 502416.0 25 | 26 | [ angles ] 27 | ; i j k funct angle force.c. 28 | 2 1 3 1 104.52 628.02 104.52 628.02 29 | 30 | #endif 31 | 32 | 33 | [ virtual_sites3 ] 34 | ; Vsite from funct a b c 35 | 4 1 2 3 4 -0.344908262 -0.34490826 -6.4437903493 36 | 5 1 2 3 4 -0.344908262 -0.34490826 6.4437903493 37 | 38 | 39 | [ exclusions ] 40 | 1 2 3 4 5 41 | 2 1 3 4 5 42 | 3 1 2 4 5 43 | 4 1 2 3 5 44 | 5 1 2 3 4 45 | 46 | 47 | ; The positions of the vsites are computed as follows: 48 | ; 49 | ; LP1 LP2 50 | ; 51 | ; O 52 | ; 53 | ; H1 H2 54 | ; 55 | ; angle A (H1-O-H2) = 104.52 56 | ; angle B (M1-O-M2) = 109.47 57 | ; dist C (H-O) = 0.09572 nm 58 | ; dist D (M-O) = 0.070 nm 59 | ; 60 | ;atom x y z 61 | ;O 0.0 0.0 0.0 62 | ;H1 0.585882276 0.756950327 0.0 63 | ;H2 0.585882276 -0.756950327 0.0 64 | ;M1 -0.404151276 0.0 0.571543301 65 | ;M2 -0.404151276 0.0 -0.571543301 66 | ; Dummy pos x4 = x1 + a4*(x2-x1) + b4*(x3-x1) + c4*((x2-x1) x (x3-x1)) 67 | ; Dummy pos x5 = x1 + a5*(x2-x1) + b5*(x3-x1) + c5*((x2-x1) x (x3-x1)) 68 | ; a4 = b4 = a5 = b5 = (D*cos(B/2)) / (2*C*cos(A/2)) = -0.34490826 69 | ; c5 = -c4 = (D * sin(B/2))/ (C^2 * sin(A)) = 6.4437903 70 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/urea.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | ; molname nrexcl 3 | URE 3 4 | 5 | [ atoms ] 6 | 1 C 1 URE C 1 0.880229 12.01000 ; amber C type 7 | 2 O 1 URE O 2 -0.613359 16.00000 ; amber O type 8 | 3 N 1 URE N1 3 -0.923545 14.01000 ; amber N type 9 | 4 H 1 URE H11 4 0.395055 1.00800 ; amber H type 10 | 5 H 1 URE H12 5 0.395055 1.00800 ; amber H type 11 | 6 N 1 URE N2 6 -0.923545 14.01000 ; amber N type 12 | 7 H 1 URE H21 7 0.395055 1.00800 ; amber H type 13 | 8 H 1 URE H22 8 0.395055 1.00800 ; amber H type 14 | 15 | [ bonds ] 16 | 1 2 17 | 1 3 18 | 1 6 19 | 3 4 20 | 3 5 21 | 6 7 22 | 6 8 23 | [ dihedrals ] 24 | ; ai aj ak al funct definition 25 | 2 1 3 4 9 26 | 2 1 3 5 9 27 | 2 1 6 7 9 28 | 2 1 6 8 9 29 | 3 1 6 7 9 30 | 3 1 6 8 9 31 | 6 1 3 4 9 32 | 6 1 3 5 9 33 | [ dihedrals ] 34 | 3 6 1 2 4 35 | 1 4 3 5 4 36 | 1 7 6 8 4 37 | -------------------------------------------------------------------------------- /stilbene_vacuum/amber14sb_OL15.ff/watermodels.dat: -------------------------------------------------------------------------------- 1 | tip3p TIP3P TIP 3-point, recommended 2 | tip4p TIP4P TIP 4-point 3 | tip4pew TIP4P-Ew TIP 4-point optimized with Ewald 4 | spc SPC simple point charge 5 | spce SPC/E extended simple point charge 6 | -------------------------------------------------------------------------------- /stilbene_vacuum/conf.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.366 10.088 10.314 4 | 1TSB H1 2 10.434 10.089 10.394 5 | 1TSB C2 3 10.397 10.005 10.205 6 | 1TSB H2 4 10.485 9.943 10.210 7 | 1TSB C3 5 10.311 9.994 10.096 8 | 1TSB H3 6 10.337 9.919 10.017 9 | 1TSB C4 7 10.201 10.080 10.089 10 | 1TSB C5 8 10.171 10.161 10.201 11 | 1TSB H5 9 10.081 10.228 10.204 12 | 1TSB C6 10 10.255 10.173 10.313 13 | 1TSB H6 11 10.230 10.239 10.395 14 | 1TSB C7 12 10.111 10.069 9.975 15 | 1TSB H7 13 10.146 10.004 9.902 16 | 1TSB C8 14 10.002 10.144 9.950 17 | 1TSB H8 15 9.980 10.222 10.027 18 | 1TSB C9 16 9.924 10.127 9.833 19 | 1TSB C10 17 9.828 10.225 9.808 20 | 1TSB H10 18 9.820 10.307 9.874 21 | 1TSB C11 19 9.750 10.225 9.684 22 | 1TSB H11 20 9.676 10.300 9.661 23 | 1TSB C12 21 9.765 10.113 9.596 24 | 1TSB H12 22 9.699 10.100 9.511 25 | 1TSB C13 23 9.853 10.010 9.624 26 | 1TSB H13 24 9.868 9.923 9.568 27 | 1TSB C14 25 9.931 10.017 9.743 28 | 1TSB H14 26 10.004 9.945 9.757 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb1.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.366 10.088 10.314 4 | 1TSB H1 2 10.434 10.089 10.394 5 | 1TSB C2 3 10.397 10.005 10.205 6 | 1TSB H2 4 10.485 9.943 10.210 7 | 1TSB C3 5 10.311 9.994 10.096 8 | 1TSB H3 6 10.337 9.919 10.017 9 | 1TSB C4 7 10.201 10.080 10.089 10 | 1TSB C5 8 10.171 10.161 10.201 11 | 1TSB H5 9 10.081 10.228 10.204 12 | 1TSB C6 10 10.255 10.173 10.313 13 | 1TSB H6 11 10.230 10.239 10.395 14 | 1TSB C7 12 10.111 10.069 9.975 15 | 1TSB H7 13 10.146 10.004 9.902 16 | 1TSB C8 14 10.002 10.144 9.950 17 | 1TSB H8 15 9.980 10.222 10.027 18 | 1TSB C9 16 9.924 10.127 9.833 19 | 1TSB C10 17 9.828 10.225 9.808 20 | 1TSB H10 18 9.820 10.307 9.874 21 | 1TSB C11 19 9.750 10.225 9.684 22 | 1TSB H11 20 9.676 10.300 9.661 23 | 1TSB C12 21 9.765 10.113 9.596 24 | 1TSB H12 22 9.699 10.100 9.511 25 | 1TSB C13 23 9.853 10.010 9.624 26 | 1TSB H13 24 9.868 9.923 9.568 27 | 1TSB C14 25 9.931 10.017 9.743 28 | 1TSB H14 26 10.004 9.945 9.757 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb10.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.288 9.989 10.336 4 | 1TSB H1 2 10.329 9.965 10.432 5 | 1TSB C2 3 10.346 9.932 10.225 6 | 1TSB H2 4 10.432 9.862 10.230 7 | 1TSB C3 5 10.291 9.972 10.103 8 | 1TSB H3 6 10.320 9.930 10.012 9 | 1TSB C4 7 10.182 10.059 10.097 10 | 1TSB C5 8 10.124 10.114 10.215 11 | 1TSB H5 9 10.035 10.183 10.212 12 | 1TSB C6 10 10.173 10.070 10.336 13 | 1TSB H6 11 10.120 10.086 10.431 14 | 1TSB C7 12 10.131 10.094 9.968 15 | 1TSB H7 13 10.172 10.030 9.895 16 | 1TSB C8 14 10.015 10.158 9.935 17 | 1TSB H8 15 9.978 10.231 10.003 18 | 1TSB C9 16 9.908 10.109 9.847 19 | 1TSB C10 17 9.795 10.192 9.831 20 | 1TSB H10 18 9.782 10.273 9.895 21 | 1TSB C11 19 9.700 10.150 9.740 22 | 1TSB H11 20 9.608 10.209 9.717 23 | 1TSB C12 21 9.727 10.038 9.658 24 | 1TSB H12 22 9.652 10.009 9.589 25 | 1TSB C13 23 9.834 9.956 9.681 26 | 1TSB H13 24 9.853 9.867 9.630 27 | 1TSB C14 25 9.933 9.996 9.767 28 | 1TSB H14 26 10.017 9.938 9.777 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb11.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.281 9.980 10.342 4 | 1TSB H1 2 10.323 9.955 10.435 5 | 1TSB C2 3 10.342 9.928 10.230 6 | 1TSB H2 4 10.416 9.858 10.241 7 | 1TSB C3 5 10.286 9.956 10.106 8 | 1TSB H3 6 10.326 9.915 10.012 9 | 1TSB C4 7 10.179 10.056 10.096 10 | 1TSB C5 8 10.142 10.128 10.211 11 | 1TSB H5 9 10.068 10.207 10.206 12 | 1TSB C6 10 10.185 10.083 10.335 13 | 1TSB H6 11 10.149 10.134 10.423 14 | 1TSB C7 12 10.130 10.098 9.965 15 | 1TSB H7 13 10.164 10.038 9.882 16 | 1TSB C8 14 10.016 10.161 9.935 17 | 1TSB H8 15 9.985 10.229 10.006 18 | 1TSB C9 16 9.912 10.104 9.852 19 | 1TSB C10 17 9.779 10.152 9.847 20 | 1TSB H10 18 9.759 10.248 9.904 21 | 1TSB C11 19 9.676 10.095 9.769 22 | 1TSB H11 20 9.578 10.135 9.781 23 | 1TSB C12 21 9.703 9.978 9.700 24 | 1TSB H12 22 9.625 9.920 9.650 25 | 1TSB C13 23 9.837 9.921 9.703 26 | 1TSB H13 24 9.849 9.823 9.671 27 | 1TSB C14 25 9.935 9.984 9.781 28 | 1TSB H14 26 10.024 9.929 9.796 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb12.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.220 9.948 10.347 4 | 1TSB H1 2 10.243 9.913 10.448 5 | 1TSB C2 3 10.316 9.934 10.245 6 | 1TSB H2 4 10.396 9.868 10.262 7 | 1TSB C3 5 10.288 9.976 10.114 8 | 1TSB H3 6 10.362 9.956 10.038 9 | 1TSB C4 7 10.167 10.053 10.094 10 | 1TSB C5 8 10.077 10.077 10.202 11 | 1TSB H5 9 9.982 10.121 10.179 12 | 1TSB C6 10 10.103 10.024 10.324 13 | 1TSB H6 11 10.026 10.031 10.401 14 | 1TSB C7 12 10.134 10.102 9.958 15 | 1TSB H7 13 10.165 10.040 9.878 16 | 1TSB C8 14 10.022 10.165 9.935 17 | 1TSB H8 15 9.999 10.253 10.007 18 | 1TSB C9 16 9.914 10.099 9.860 19 | 1TSB C10 17 9.790 10.161 9.865 20 | 1TSB H10 18 9.779 10.262 9.896 21 | 1TSB C11 19 9.669 10.089 9.833 22 | 1TSB H11 20 9.570 10.135 9.835 23 | 1TSB C12 21 9.680 9.959 9.780 24 | 1TSB H12 22 9.594 9.909 9.733 25 | 1TSB C13 23 9.807 9.901 9.773 26 | 1TSB H13 24 9.808 9.806 9.727 27 | 1TSB C14 25 9.924 9.964 9.816 28 | 1TSB H14 26 10.013 9.896 9.820 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb13.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.262 9.937 10.342 4 | 1TSB H1 2 10.295 9.890 10.434 5 | 1TSB C2 3 10.337 9.921 10.224 6 | 1TSB H2 4 10.427 9.852 10.226 7 | 1TSB C3 5 10.294 9.980 10.105 8 | 1TSB H3 6 10.348 9.953 10.012 9 | 1TSB C4 7 10.174 10.050 10.095 10 | 1TSB C5 8 10.104 10.068 10.219 11 | 1TSB H5 9 10.008 10.121 10.218 12 | 1TSB C6 10 10.140 10.004 10.337 13 | 1TSB H6 11 10.079 10.010 10.425 14 | 1TSB C7 12 10.136 10.104 9.967 15 | 1TSB H7 13 10.164 10.038 9.891 16 | 1TSB C8 14 10.016 10.165 9.929 17 | 1TSB H8 15 9.979 10.248 9.991 18 | 1TSB C9 16 9.911 10.100 9.856 19 | 1TSB C10 17 9.779 10.147 9.886 20 | 1TSB H10 18 9.756 10.215 9.961 21 | 1TSB C11 19 9.667 10.091 9.829 22 | 1TSB H11 20 9.567 10.129 9.850 23 | 1TSB C12 21 9.681 9.982 9.740 24 | 1TSB H12 22 9.593 9.932 9.696 25 | 1TSB C13 23 9.807 9.934 9.716 26 | 1TSB H13 24 9.818 9.847 9.650 27 | 1TSB C14 25 9.924 9.992 9.766 28 | 1TSB H14 26 10.016 9.949 9.743 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb14.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.231 9.916 10.327 4 | 1TSB H1 2 10.255 9.868 10.423 5 | 1TSB C2 3 10.297 9.882 10.214 6 | 1TSB H2 4 10.377 9.809 10.212 7 | 1TSB C3 5 10.271 9.957 10.094 8 | 1TSB H3 6 10.308 9.924 10.004 9 | 1TSB C4 7 10.166 10.049 10.088 10 | 1TSB C5 8 10.094 10.073 10.205 11 | 1TSB H5 9 10.014 10.145 10.202 12 | 1TSB C6 10 10.129 10.015 10.326 13 | 1TSB H6 11 10.085 10.045 10.421 14 | 1TSB C7 12 10.135 10.107 9.966 15 | 1TSB H7 13 10.197 10.060 9.884 16 | 1TSB C8 14 10.017 10.168 9.929 17 | 1TSB H8 15 9.972 10.232 10.008 18 | 1TSB C9 16 9.919 10.095 9.864 19 | 1TSB C10 17 9.784 10.141 9.859 20 | 1TSB H10 18 9.758 10.229 9.915 21 | 1TSB C11 19 9.678 10.071 9.796 22 | 1TSB H11 20 9.579 10.108 9.809 23 | 1TSB C12 21 9.703 9.948 9.730 24 | 1TSB H12 22 9.639 9.871 9.694 25 | 1TSB C13 23 9.834 9.902 9.734 26 | 1TSB H13 24 9.856 9.796 9.700 27 | 1TSB C14 25 9.942 9.973 9.799 28 | 1TSB H14 26 10.040 9.934 9.802 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb15.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.204 9.930 10.337 4 | 1TSB H1 2 10.217 9.902 10.438 5 | 1TSB C2 3 10.313 9.955 10.251 6 | 1TSB H2 4 10.414 9.922 10.278 7 | 1TSB C3 5 10.286 10.025 10.137 8 | 1TSB H3 6 10.367 10.061 10.081 9 | 1TSB C4 7 10.157 10.041 10.090 10 | 1TSB C5 8 10.045 9.992 10.169 11 | 1TSB H5 9 9.946 10.002 10.123 12 | 1TSB C6 10 10.068 9.944 10.302 13 | 1TSB H6 11 9.989 9.919 10.364 14 | 1TSB C7 12 10.141 10.116 9.961 15 | 1TSB H7 13 10.223 10.183 9.937 16 | 1TSB C8 14 10.024 10.173 9.924 17 | 1TSB H8 15 10.026 10.275 9.888 18 | 1TSB C9 16 9.915 10.089 9.871 19 | 1TSB C10 17 9.798 10.162 9.839 20 | 1TSB H10 18 9.808 10.274 9.842 21 | 1TSB C11 19 9.679 10.103 9.798 22 | 1TSB H11 20 9.592 10.160 9.764 23 | 1TSB C12 21 9.681 9.961 9.785 24 | 1TSB H12 22 9.591 9.907 9.760 25 | 1TSB C13 23 9.801 9.893 9.807 26 | 1TSB H13 24 9.812 9.786 9.802 27 | 1TSB C14 25 9.915 9.951 9.855 28 | 1TSB H14 26 10.004 9.904 9.869 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb16.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.194 9.902 10.328 4 | 1TSB H1 2 10.213 9.856 10.421 5 | 1TSB C2 3 10.304 9.924 10.241 6 | 1TSB H2 4 10.404 9.895 10.274 7 | 1TSB C3 5 10.284 9.992 10.121 8 | 1TSB H3 6 10.363 10.017 10.056 9 | 1TSB C4 7 10.158 10.041 10.088 10 | 1TSB C5 8 10.047 10.028 10.181 11 | 1TSB H5 9 9.953 10.076 10.162 12 | 1TSB C6 10 10.068 9.959 10.303 13 | 1TSB H6 11 9.988 9.948 10.373 14 | 1TSB C7 12 10.144 10.117 9.969 15 | 1TSB H7 13 10.228 10.179 9.949 16 | 1TSB C8 14 10.024 10.171 9.924 17 | 1TSB H8 15 10.043 10.271 9.888 18 | 1TSB C9 16 9.910 10.091 9.866 19 | 1TSB C10 17 9.794 10.143 9.809 20 | 1TSB H10 18 9.784 10.250 9.796 21 | 1TSB C11 19 9.694 10.063 9.758 22 | 1TSB H11 20 9.604 10.114 9.730 23 | 1TSB C12 21 9.701 9.924 9.753 24 | 1TSB H12 22 9.622 9.861 9.707 25 | 1TSB C13 23 9.818 9.866 9.805 26 | 1TSB H13 24 9.831 9.760 9.794 27 | 1TSB C14 25 9.921 9.949 9.856 28 | 1TSB H14 26 10.013 9.910 9.888 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb17.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.195 9.857 10.295 4 | 1TSB H1 2 10.215 9.791 10.374 5 | 1TSB C2 3 10.303 9.907 10.221 6 | 1TSB H2 4 10.398 9.890 10.252 7 | 1TSB C3 5 10.285 9.996 10.114 8 | 1TSB H3 6 10.366 10.022 10.045 9 | 1TSB C4 7 10.156 10.040 10.085 10 | 1TSB C5 8 10.048 10.002 10.168 11 | 1TSB H5 9 9.950 10.035 10.140 12 | 1TSB C6 10 10.070 9.915 10.275 13 | 1TSB H6 11 9.986 9.885 10.338 14 | 1TSB C7 12 10.142 10.120 9.969 15 | 1TSB H7 13 10.231 10.182 9.944 16 | 1TSB C8 14 10.025 10.171 9.924 17 | 1TSB H8 15 10.028 10.276 9.879 18 | 1TSB C9 16 9.914 10.088 9.870 19 | 1TSB C10 17 9.798 10.156 9.838 20 | 1TSB H10 18 9.777 10.262 9.857 21 | 1TSB C11 19 9.685 10.082 9.794 22 | 1TSB H11 20 9.598 10.134 9.776 23 | 1TSB C12 21 9.692 9.943 9.779 24 | 1TSB H12 22 9.608 9.883 9.746 25 | 1TSB C13 23 9.811 9.880 9.809 26 | 1TSB H13 24 9.824 9.773 9.795 27 | 1TSB C14 25 9.928 9.953 9.844 28 | 1TSB H14 26 10.011 9.900 9.868 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb18.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.187 9.886 10.322 4 | 1TSB H1 2 10.209 9.825 10.409 5 | 1TSB C2 3 10.299 9.930 10.250 6 | 1TSB H2 4 10.402 9.905 10.279 7 | 1TSB C3 5 10.277 10.026 10.151 8 | 1TSB H3 6 10.360 10.079 10.103 9 | 1TSB C4 7 10.153 10.040 10.087 10 | 1TSB C5 8 10.040 9.977 10.153 11 | 1TSB H5 9 9.939 9.989 10.116 12 | 1TSB C6 10 10.054 9.900 10.265 13 | 1TSB H6 11 9.966 9.852 10.306 14 | 1TSB C7 12 10.144 10.122 9.969 15 | 1TSB H7 13 10.223 10.192 9.960 16 | 1TSB C8 14 10.027 10.165 9.917 17 | 1TSB H8 15 10.030 10.272 9.887 18 | 1TSB C9 16 9.912 10.092 9.874 19 | 1TSB C10 17 9.783 10.143 9.859 20 | 1TSB H10 18 9.769 10.249 9.872 21 | 1TSB C11 19 9.674 10.062 9.808 22 | 1TSB H11 20 9.577 10.104 9.785 23 | 1TSB C12 21 9.693 9.925 9.799 24 | 1TSB H12 22 9.617 9.853 9.776 25 | 1TSB C13 23 9.825 9.873 9.825 26 | 1TSB H13 24 9.833 9.768 9.823 27 | 1TSB C14 25 9.936 9.956 9.855 28 | 1TSB H14 26 10.032 9.912 9.863 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb19.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.207 9.845 10.303 4 | 1TSB H1 2 10.224 9.783 10.391 5 | 1TSB C2 3 10.315 9.917 10.239 6 | 1TSB H2 4 10.416 9.907 10.273 7 | 1TSB C3 5 10.286 10.011 10.138 8 | 1TSB H3 6 10.373 10.066 10.092 9 | 1TSB C4 7 10.158 10.035 10.086 10 | 1TSB C5 8 10.049 9.967 10.149 11 | 1TSB H5 9 9.951 9.984 10.120 12 | 1TSB C6 10 10.077 9.875 10.256 13 | 1TSB H6 11 9.995 9.816 10.301 14 | 1TSB C7 12 10.140 10.128 9.973 15 | 1TSB H7 13 10.222 10.191 9.965 16 | 1TSB C8 14 10.025 10.169 9.915 17 | 1TSB H8 15 10.029 10.268 9.880 18 | 1TSB C9 16 9.914 10.088 9.874 19 | 1TSB C10 17 9.799 10.159 9.832 20 | 1TSB H10 18 9.799 10.264 9.828 21 | 1TSB C11 19 9.683 10.093 9.787 22 | 1TSB H11 20 9.598 10.150 9.757 23 | 1TSB C12 21 9.674 9.958 9.800 24 | 1TSB H12 22 9.589 9.904 9.763 25 | 1TSB C13 23 9.787 9.879 9.840 26 | 1TSB H13 24 9.783 9.771 9.846 27 | 1TSB C14 25 9.911 9.945 9.863 28 | 1TSB H14 26 10.005 9.885 9.890 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb2.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.334 10.083 10.332 4 | 1TSB H1 2 10.397 10.091 10.416 5 | 1TSB C2 3 10.387 10.018 10.223 6 | 1TSB H2 4 10.485 9.980 10.233 7 | 1TSB C3 5 10.321 10.022 10.101 8 | 1TSB H3 6 10.366 9.981 10.010 9 | 1TSB C4 7 10.193 10.081 10.093 10 | 1TSB C5 8 10.137 10.138 10.207 11 | 1TSB H5 9 10.037 10.178 10.212 12 | 1TSB C6 10 10.213 10.146 10.325 13 | 1TSB H6 11 10.174 10.189 10.411 14 | 1TSB C7 12 10.122 10.069 9.973 15 | 1TSB H7 13 10.164 10.006 9.891 16 | 1TSB C8 14 10.008 10.140 9.947 17 | 1TSB H8 15 9.993 10.214 10.022 18 | 1TSB C9 16 9.914 10.129 9.835 19 | 1TSB C10 17 9.798 10.215 9.843 20 | 1TSB H10 18 9.782 10.274 9.928 21 | 1TSB C11 19 9.707 10.222 9.743 22 | 1TSB H11 20 9.617 10.280 9.752 23 | 1TSB C12 21 9.727 10.140 9.628 24 | 1TSB H12 22 9.660 10.146 9.543 25 | 1TSB C13 23 9.837 10.054 9.621 26 | 1TSB H13 24 9.846 9.973 9.540 27 | 1TSB C14 25 9.939 10.049 9.724 28 | 1TSB H14 26 10.029 9.982 9.717 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb20.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.186 9.875 10.316 4 | 1TSB H1 2 10.206 9.819 10.404 5 | 1TSB C2 3 10.297 9.926 10.244 6 | 1TSB H2 4 10.389 9.910 10.288 7 | 1TSB C3 5 10.279 10.004 10.136 8 | 1TSB H3 6 10.363 10.049 10.085 9 | 1TSB C4 7 10.155 10.035 10.083 10 | 1TSB C5 8 10.049 9.976 10.157 11 | 1TSB H5 9 9.951 10.003 10.123 12 | 1TSB C6 10 10.057 9.893 10.273 13 | 1TSB H6 11 9.964 9.861 10.320 14 | 1TSB C7 12 10.144 10.127 9.976 15 | 1TSB H7 13 10.225 10.198 9.970 16 | 1TSB C8 14 10.027 10.169 9.916 17 | 1TSB H8 15 10.029 10.266 9.873 18 | 1TSB C9 16 9.911 10.088 9.871 19 | 1TSB C10 17 9.796 10.156 9.826 20 | 1TSB H10 18 9.801 10.267 9.831 21 | 1TSB C11 19 9.700 10.082 9.760 22 | 1TSB H11 20 9.605 10.129 9.728 23 | 1TSB C12 21 9.719 9.942 9.739 24 | 1TSB H12 22 9.648 9.879 9.683 25 | 1TSB C13 23 9.831 9.874 9.782 26 | 1TSB H13 24 9.842 9.765 9.770 27 | 1TSB C14 25 9.928 9.952 9.851 28 | 1TSB H14 26 10.023 9.908 9.871 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb21.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.181 9.871 10.309 4 | 1TSB H1 2 10.188 9.808 10.395 5 | 1TSB C2 3 10.297 9.921 10.246 6 | 1TSB H2 4 10.392 9.898 10.285 7 | 1TSB C3 5 10.281 10.012 10.135 8 | 1TSB H3 6 10.373 10.055 10.090 9 | 1TSB C4 7 10.152 10.034 10.082 10 | 1TSB C5 8 10.039 9.980 10.152 11 | 1TSB H5 9 9.942 10.013 10.131 12 | 1TSB C6 10 10.053 9.894 10.260 13 | 1TSB H6 11 9.967 9.859 10.309 14 | 1TSB C7 12 10.143 10.130 9.974 15 | 1TSB H7 13 10.227 10.201 9.966 16 | 1TSB C8 14 10.029 10.168 9.915 17 | 1TSB H8 15 10.035 10.268 9.865 18 | 1TSB C9 16 9.913 10.087 9.876 19 | 1TSB C10 17 9.802 10.160 9.823 20 | 1TSB H10 18 9.805 10.265 9.815 21 | 1TSB C11 19 9.694 10.091 9.772 22 | 1TSB H11 20 9.603 10.140 9.741 23 | 1TSB C12 21 9.691 9.948 9.794 24 | 1TSB H12 22 9.604 9.890 9.773 25 | 1TSB C13 23 9.793 9.878 9.847 26 | 1TSB H13 24 9.797 9.768 9.846 27 | 1TSB C14 25 9.902 9.945 9.884 28 | 1TSB H14 26 9.984 9.888 9.928 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb22.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.217 9.834 10.279 4 | 1TSB H1 2 10.237 9.753 10.348 5 | 1TSB C2 3 10.331 9.907 10.220 6 | 1TSB H2 4 10.431 9.876 10.243 7 | 1TSB C3 5 10.298 10.009 10.122 8 | 1TSB H3 6 10.384 10.062 10.081 9 | 1TSB C4 7 10.161 10.029 10.082 10 | 1TSB C5 8 10.055 9.956 10.145 11 | 1TSB H5 9 9.951 9.963 10.105 12 | 1TSB C6 10 10.086 9.859 10.244 13 | 1TSB H6 11 10.007 9.797 10.288 14 | 1TSB C7 12 10.140 10.134 9.982 15 | 1TSB H7 13 10.212 10.210 9.984 16 | 1TSB C8 14 10.024 10.173 9.913 17 | 1TSB H8 15 10.030 10.273 9.864 18 | 1TSB C9 16 9.912 10.084 9.870 19 | 1TSB C10 17 9.797 10.149 9.812 20 | 1TSB H10 18 9.796 10.257 9.812 21 | 1TSB C11 19 9.684 10.073 9.770 22 | 1TSB H11 20 9.601 10.129 9.734 23 | 1TSB C12 21 9.700 9.931 9.758 24 | 1TSB H12 22 9.621 9.877 9.706 25 | 1TSB C13 23 9.814 9.862 9.813 26 | 1TSB H13 24 9.828 9.756 9.789 27 | 1TSB C14 25 9.918 9.943 9.862 28 | 1TSB H14 26 10.017 9.900 9.883 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb23.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.207 9.840 10.283 4 | 1TSB H1 2 10.233 9.753 10.348 5 | 1TSB C2 3 10.318 9.914 10.229 6 | 1TSB H2 4 10.421 9.897 10.267 7 | 1TSB C3 5 10.291 10.012 10.132 8 | 1TSB H3 6 10.371 10.076 10.090 9 | 1TSB C4 7 10.162 10.031 10.085 10 | 1TSB C5 8 10.056 9.962 10.146 11 | 1TSB H5 9 9.957 9.993 10.112 12 | 1TSB C6 10 10.076 9.862 10.244 13 | 1TSB H6 11 9.996 9.793 10.276 14 | 1TSB C7 12 10.140 10.134 9.982 15 | 1TSB H7 13 10.221 10.210 9.984 16 | 1TSB C8 14 10.028 10.167 9.913 17 | 1TSB H8 15 10.035 10.267 9.880 18 | 1TSB C9 16 9.907 10.088 9.867 19 | 1TSB C10 17 9.796 10.155 9.810 20 | 1TSB H10 18 9.788 10.260 9.816 21 | 1TSB C11 19 9.683 10.084 9.771 22 | 1TSB H11 20 9.596 10.144 9.749 23 | 1TSB C12 21 9.682 9.943 9.768 24 | 1TSB H12 22 9.591 9.899 9.731 25 | 1TSB C13 23 9.790 9.875 9.825 26 | 1TSB H13 24 9.786 9.769 9.835 27 | 1TSB C14 25 9.905 9.946 9.866 28 | 1TSB H14 26 9.991 9.890 9.886 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb24.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.192 9.823 10.273 4 | 1TSB H1 2 10.202 9.742 10.341 5 | 1TSB C2 3 10.301 9.884 10.212 6 | 1TSB H2 4 10.396 9.849 10.243 7 | 1TSB C3 5 10.284 9.991 10.123 8 | 1TSB H3 6 10.369 10.039 10.077 9 | 1TSB C4 7 10.157 10.031 10.078 10 | 1TSB C5 8 10.051 9.983 10.155 11 | 1TSB H5 9 9.950 10.012 10.122 12 | 1TSB C6 10 10.064 9.876 10.251 13 | 1TSB H6 11 9.977 9.831 10.294 14 | 1TSB C7 12 10.139 10.136 9.986 15 | 1TSB H7 13 10.209 10.219 10.000 16 | 1TSB C8 14 10.030 10.164 9.912 17 | 1TSB H8 15 10.048 10.262 9.865 18 | 1TSB C9 16 9.911 10.088 9.871 19 | 1TSB C10 17 9.802 10.159 9.831 20 | 1TSB H10 18 9.808 10.269 9.828 21 | 1TSB C11 19 9.687 10.089 9.791 22 | 1TSB H11 20 9.600 10.137 9.754 23 | 1TSB C12 21 9.685 9.954 9.795 24 | 1TSB H12 22 9.600 9.894 9.779 25 | 1TSB C13 23 9.794 9.878 9.840 26 | 1TSB H13 24 9.796 9.767 9.843 27 | 1TSB C14 25 9.908 9.950 9.876 28 | 1TSB H14 26 9.999 9.889 9.902 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb25.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.253 9.812 10.243 4 | 1TSB H1 2 10.287 9.731 10.303 5 | 1TSB C2 3 10.342 9.911 10.206 6 | 1TSB H2 4 10.446 9.903 10.236 7 | 1TSB C3 5 10.296 10.023 10.135 8 | 1TSB H3 6 10.366 10.105 10.124 9 | 1TSB C4 7 10.163 10.025 10.075 10 | 1TSB C5 8 10.079 9.924 10.115 11 | 1TSB H5 9 9.970 9.927 10.097 12 | 1TSB C6 10 10.117 9.817 10.198 13 | 1TSB H6 11 10.038 9.752 10.243 14 | 1TSB C7 12 10.133 10.142 9.992 15 | 1TSB H7 13 10.199 10.224 10.002 16 | 1TSB C8 14 10.027 10.170 9.912 17 | 1TSB H8 15 10.030 10.274 9.883 18 | 1TSB C9 16 9.914 10.082 9.868 19 | 1TSB C10 17 9.786 10.133 9.844 20 | 1TSB H10 18 9.772 10.237 9.869 21 | 1TSB C11 19 9.682 10.049 9.804 22 | 1TSB H11 20 9.579 10.091 9.792 23 | 1TSB C12 21 9.706 9.917 9.770 24 | 1TSB H12 22 9.628 9.855 9.733 25 | 1TSB C13 23 9.832 9.863 9.794 26 | 1TSB H13 24 9.853 9.756 9.781 27 | 1TSB C14 25 9.937 9.947 9.847 28 | 1TSB H14 26 10.036 9.901 9.867 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb26.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.232 9.833 10.273 4 | 1TSB H1 2 10.261 9.740 10.328 5 | 1TSB C2 3 10.332 9.910 10.210 6 | 1TSB H2 4 10.437 9.889 10.233 7 | 1TSB C3 5 10.297 10.009 10.119 8 | 1TSB H3 6 10.377 10.078 10.076 9 | 1TSB C4 7 10.165 10.028 10.078 10 | 1TSB C5 8 10.065 9.960 10.146 11 | 1TSB H5 9 9.956 9.982 10.135 12 | 1TSB C6 10 10.102 9.859 10.238 13 | 1TSB H6 11 10.030 9.792 10.283 14 | 1TSB C7 12 10.133 10.139 9.991 15 | 1TSB H7 13 10.216 10.210 9.984 16 | 1TSB C8 14 10.027 10.165 9.911 17 | 1TSB H8 15 10.039 10.257 9.858 18 | 1TSB C9 16 9.912 10.087 9.867 19 | 1TSB C10 17 9.813 10.154 9.796 20 | 1TSB H10 18 9.815 10.265 9.795 21 | 1TSB C11 19 9.711 10.082 9.728 22 | 1TSB H11 20 9.626 10.132 9.683 23 | 1TSB C12 21 9.709 9.945 9.732 24 | 1TSB H12 22 9.633 9.888 9.679 25 | 1TSB C13 23 9.809 9.874 9.794 26 | 1TSB H13 24 9.811 9.764 9.785 27 | 1TSB C14 25 9.913 9.947 9.859 28 | 1TSB H14 26 9.994 9.890 9.893 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb27.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.264 9.823 10.259 4 | 1TSB H1 2 10.302 9.757 10.334 5 | 1TSB C2 3 10.351 9.915 10.211 6 | 1TSB H2 4 10.456 9.910 10.242 7 | 1TSB C3 5 10.307 10.021 10.121 8 | 1TSB H3 6 10.380 10.095 10.083 9 | 1TSB C4 7 10.172 10.028 10.079 10 | 1TSB C5 8 10.090 9.929 10.127 11 | 1TSB H5 9 9.991 9.929 10.090 12 | 1TSB C6 10 10.129 9.831 10.221 13 | 1TSB H6 11 10.047 9.773 10.267 14 | 1TSB C7 12 10.130 10.139 9.995 15 | 1TSB H7 13 10.195 10.222 10.014 16 | 1TSB C8 14 10.026 10.162 9.911 17 | 1TSB H8 15 10.020 10.271 9.895 18 | 1TSB C9 16 9.910 10.090 9.862 19 | 1TSB C10 17 9.815 10.163 9.787 20 | 1TSB H10 18 9.823 10.269 9.772 21 | 1TSB C11 19 9.698 10.101 9.734 22 | 1TSB H11 20 9.616 10.164 9.698 23 | 1TSB C12 21 9.685 9.959 9.751 24 | 1TSB H12 22 9.601 9.905 9.717 25 | 1TSB C13 23 9.787 9.889 9.808 26 | 1TSB H13 24 9.779 9.777 9.811 27 | 1TSB C14 25 9.905 9.949 9.849 28 | 1TSB H14 26 9.985 9.886 9.877 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb28.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.254 9.794 10.215 4 | 1TSB H1 2 10.285 9.705 10.273 5 | 1TSB C2 3 10.345 9.885 10.162 6 | 1TSB H2 4 10.452 9.883 10.177 7 | 1TSB C3 5 10.302 9.995 10.082 8 | 1TSB H3 6 10.370 10.077 10.059 9 | 1TSB C4 7 10.163 10.023 10.066 10 | 1TSB C5 8 10.070 9.937 10.119 11 | 1TSB H5 9 9.969 9.966 10.105 12 | 1TSB C6 10 10.116 9.813 10.178 13 | 1TSB H6 11 10.042 9.752 10.224 14 | 1TSB C7 12 10.128 10.145 10.000 15 | 1TSB H7 13 10.198 10.228 10.005 16 | 1TSB C8 14 10.026 10.170 9.912 17 | 1TSB H8 15 10.018 10.272 9.876 18 | 1TSB C9 16 9.920 10.081 9.868 19 | 1TSB C10 17 9.797 10.132 9.832 20 | 1TSB H10 18 9.782 10.236 9.831 21 | 1TSB C11 19 9.693 10.044 9.789 22 | 1TSB H11 20 9.597 10.085 9.771 23 | 1TSB C12 21 9.719 9.912 9.765 24 | 1TSB H12 22 9.640 9.845 9.722 25 | 1TSB C13 23 9.847 9.863 9.790 26 | 1TSB H13 24 9.872 9.763 9.779 27 | 1TSB C14 25 9.946 9.947 9.846 28 | 1TSB H14 26 10.040 9.895 9.857 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb29.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.317 9.787 10.140 4 | 1TSB H1 2 10.362 9.700 10.177 5 | 1TSB C2 3 10.383 9.914 10.136 6 | 1TSB H2 4 10.493 9.908 10.158 7 | 1TSB C3 5 10.317 10.031 10.103 8 | 1TSB H3 6 10.369 10.117 10.109 9 | 1TSB C4 7 10.181 10.023 10.065 10 | 1TSB C5 8 10.110 9.906 10.076 11 | 1TSB H5 9 9.997 9.910 10.073 12 | 1TSB C6 10 10.181 9.788 10.114 13 | 1TSB H6 11 10.129 9.689 10.122 14 | 1TSB C7 12 10.113 10.143 10.009 15 | 1TSB H7 13 10.165 10.232 10.034 16 | 1TSB C8 14 10.020 10.171 9.919 17 | 1TSB H8 15 10.002 10.276 9.915 18 | 1TSB C9 16 9.923 10.082 9.855 19 | 1TSB C10 17 9.799 10.137 9.809 20 | 1TSB H10 18 9.788 10.243 9.810 21 | 1TSB C11 19 9.718 10.066 9.724 22 | 1TSB H11 20 9.628 10.110 9.680 23 | 1TSB C12 21 9.747 9.931 9.703 24 | 1TSB H12 22 9.680 9.878 9.636 25 | 1TSB C13 23 9.863 9.867 9.750 26 | 1TSB H13 24 9.890 9.771 9.726 27 | 1TSB C14 25 9.953 9.948 9.818 28 | 1TSB H14 26 10.051 9.899 9.831 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb3.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.377 10.067 10.323 4 | 1TSB H1 2 10.449 10.066 10.409 5 | 1TSB C2 3 10.393 9.975 10.220 6 | 1TSB H2 4 10.475 9.900 10.240 7 | 1TSB C3 5 10.307 9.975 10.107 8 | 1TSB H3 6 10.321 9.912 10.029 9 | 1TSB C4 7 10.200 10.073 10.094 10 | 1TSB C5 8 10.186 10.164 10.201 11 | 1TSB H5 9 10.106 10.241 10.205 12 | 1TSB C6 10 10.273 10.168 10.308 13 | 1TSB H6 11 10.253 10.236 10.390 14 | 1TSB C7 12 10.118 10.075 9.976 15 | 1TSB H7 13 10.146 10.001 9.904 16 | 1TSB C8 14 10.004 10.147 9.945 17 | 1TSB H8 15 9.980 10.223 10.017 18 | 1TSB C9 16 9.915 10.123 9.833 19 | 1TSB C10 17 9.819 10.219 9.808 20 | 1TSB H10 18 9.812 10.308 9.864 21 | 1TSB C11 19 9.741 10.211 9.686 22 | 1TSB H11 20 9.670 10.289 9.655 23 | 1TSB C12 21 9.751 10.098 9.600 24 | 1TSB H12 22 9.694 10.088 9.509 25 | 1TSB C13 23 9.842 9.997 9.629 26 | 1TSB H13 24 9.851 9.912 9.562 27 | 1TSB C14 25 9.917 10.010 9.747 28 | 1TSB H14 26 9.984 9.932 9.769 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb30.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.281 9.792 10.196 4 | 1TSB H1 2 10.327 9.709 10.242 5 | 1TSB C2 3 10.203 9.783 10.073 6 | 1TSB H2 4 10.197 9.686 10.023 7 | 1TSB C3 5 10.155 9.898 10.012 8 | 1TSB H3 6 10.111 9.897 9.914 9 | 1TSB C4 7 10.173 10.021 10.072 10 | 1TSB C5 8 10.245 10.033 10.193 11 | 1TSB H5 9 10.271 10.136 10.235 12 | 1TSB C6 10 10.302 9.921 10.246 13 | 1TSB H6 11 10.367 9.929 10.334 14 | 1TSB C7 12 10.123 10.148 10.002 15 | 1TSB H7 13 10.183 10.237 10.022 16 | 1TSB C8 14 10.024 10.167 9.908 17 | 1TSB H8 15 10.028 10.268 9.866 18 | 1TSB C9 16 9.917 10.083 9.864 19 | 1TSB C10 17 9.854 10.120 9.741 20 | 1TSB H10 18 9.887 10.206 9.694 21 | 1TSB C11 19 9.743 10.040 9.692 22 | 1TSB H11 20 9.696 10.067 9.603 23 | 1TSB C12 21 9.706 9.916 9.758 24 | 1TSB H12 22 9.632 9.847 9.722 25 | 1TSB C13 23 9.761 9.889 9.882 26 | 1TSB H13 24 9.717 9.807 9.938 27 | 1TSB C14 25 9.860 9.978 9.935 28 | 1TSB H14 26 9.896 9.953 10.042 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb4.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.377 10.052 10.304 4 | 1TSB H1 2 10.452 10.042 10.380 5 | 1TSB C2 3 10.373 9.951 10.205 6 | 1TSB H2 4 10.440 9.866 10.211 7 | 1TSB C3 5 10.281 9.958 10.101 8 | 1TSB H3 6 10.284 9.883 10.022 9 | 1TSB C4 7 10.196 10.071 10.095 10 | 1TSB C5 8 10.190 10.162 10.197 11 | 1TSB H5 9 10.132 10.253 10.195 12 | 1TSB C6 10 10.279 10.152 10.304 13 | 1TSB H6 11 10.286 10.229 10.378 14 | 1TSB C7 12 10.122 10.078 9.974 15 | 1TSB H7 13 10.149 10.008 9.896 16 | 1TSB C8 14 10.004 10.149 9.940 17 | 1TSB H8 15 9.970 10.205 10.028 18 | 1TSB C9 16 9.915 10.121 9.838 19 | 1TSB C10 17 9.776 10.147 9.853 20 | 1TSB H10 18 9.743 10.186 9.949 21 | 1TSB C11 19 9.686 10.120 9.753 22 | 1TSB H11 20 9.583 10.147 9.769 23 | 1TSB C12 21 9.733 10.081 9.625 24 | 1TSB H12 22 9.668 10.076 9.541 25 | 1TSB C13 23 9.873 10.058 9.607 26 | 1TSB H13 24 9.915 10.028 9.511 27 | 1TSB C14 25 9.965 10.083 9.716 28 | 1TSB H14 26 10.074 10.085 9.704 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb5.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.338 10.058 10.335 4 | 1TSB H1 2 10.396 10.048 10.427 5 | 1TSB C2 3 10.345 9.953 10.241 6 | 1TSB H2 4 10.417 9.873 10.268 7 | 1TSB C3 5 10.268 9.960 10.122 8 | 1TSB H3 6 10.275 9.887 10.044 9 | 1TSB C4 7 10.190 10.072 10.097 10 | 1TSB C5 8 10.189 10.182 10.188 11 | 1TSB H5 9 10.121 10.271 10.178 12 | 1TSB C6 10 10.262 10.170 10.306 13 | 1TSB H6 11 10.267 10.256 10.379 14 | 1TSB C7 12 10.127 10.079 9.970 15 | 1TSB H7 13 10.160 10.004 9.901 16 | 1TSB C8 14 10.010 10.147 9.941 17 | 1TSB H8 15 9.966 10.210 10.021 18 | 1TSB C9 16 9.910 10.121 9.840 19 | 1TSB C10 17 9.792 10.202 9.849 20 | 1TSB H10 18 9.783 10.282 9.919 21 | 1TSB C11 19 9.683 10.169 9.764 22 | 1TSB H11 20 9.598 10.227 9.765 23 | 1TSB C12 21 9.696 10.069 9.670 24 | 1TSB H12 22 9.614 10.049 9.603 25 | 1TSB C13 23 9.814 10.001 9.654 26 | 1TSB H13 24 9.820 9.914 9.588 27 | 1TSB C14 25 9.920 10.032 9.737 28 | 1TSB H14 26 10.002 9.972 9.727 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb6.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.312 10.021 10.333 4 | 1TSB H1 2 10.340 9.986 10.436 5 | 1TSB C2 3 10.347 9.939 10.227 6 | 1TSB H2 4 10.409 9.854 10.255 7 | 1TSB C3 5 10.281 9.962 10.105 8 | 1TSB H3 6 10.306 9.903 10.017 9 | 1TSB C4 7 10.189 10.067 10.094 10 | 1TSB C5 8 10.158 10.152 10.202 11 | 1TSB H5 9 10.080 10.223 10.200 12 | 1TSB C6 10 10.229 10.132 10.317 13 | 1TSB H6 11 10.199 10.192 10.404 14 | 1TSB C7 12 10.125 10.085 9.973 15 | 1TSB H7 13 10.157 10.015 9.895 16 | 1TSB C8 14 10.012 10.149 9.940 17 | 1TSB H8 15 9.976 10.221 10.013 18 | 1TSB C9 16 9.910 10.118 9.840 19 | 1TSB C10 17 9.803 10.203 9.822 20 | 1TSB H10 18 9.786 10.287 9.895 21 | 1TSB C11 19 9.719 10.183 9.710 22 | 1TSB H11 20 9.641 10.251 9.694 23 | 1TSB C12 21 9.744 10.085 9.610 24 | 1TSB H12 22 9.699 10.095 9.514 25 | 1TSB C13 23 9.838 9.987 9.637 26 | 1TSB H13 24 9.846 9.904 9.566 27 | 1TSB C14 25 9.921 10.004 9.753 28 | 1TSB H14 26 10.000 9.930 9.779 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb7.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.301 10.013 10.344 4 | 1TSB H1 2 10.338 9.977 10.442 5 | 1TSB C2 3 10.351 9.953 10.228 6 | 1TSB H2 4 10.426 9.871 10.248 7 | 1TSB C3 5 10.287 9.976 10.105 8 | 1TSB H3 6 10.309 9.918 10.020 9 | 1TSB C4 7 10.186 10.069 10.095 10 | 1TSB C5 8 10.145 10.143 10.211 11 | 1TSB H5 9 10.067 10.222 10.210 12 | 1TSB C6 10 10.199 10.109 10.335 13 | 1TSB H6 11 10.171 10.155 10.424 14 | 1TSB C7 12 10.128 10.082 9.968 15 | 1TSB H7 13 10.152 10.018 9.892 16 | 1TSB C8 14 10.011 10.151 9.941 17 | 1TSB H8 15 9.976 10.217 10.018 18 | 1TSB C9 16 9.912 10.117 9.843 19 | 1TSB C10 17 9.786 10.180 9.853 20 | 1TSB H10 18 9.751 10.248 9.936 21 | 1TSB C11 19 9.679 10.153 9.766 22 | 1TSB H11 20 9.587 10.213 9.774 23 | 1TSB C12 21 9.703 10.070 9.652 24 | 1TSB H12 22 9.626 10.052 9.577 25 | 1TSB C13 23 9.829 10.014 9.636 26 | 1TSB H13 24 9.860 9.958 9.547 27 | 1TSB C14 25 9.934 10.042 9.729 28 | 1TSB H14 26 10.031 10.002 9.705 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb8.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.279 10.020 10.359 4 | 1TSB H1 2 10.317 10.011 10.459 5 | 1TSB C2 3 10.339 9.954 10.251 6 | 1TSB H2 4 10.421 9.887 10.260 7 | 1TSB C3 5 10.292 9.979 10.120 8 | 1TSB H3 6 10.345 9.928 10.040 9 | 1TSB C4 7 10.183 10.066 10.098 10 | 1TSB C5 8 10.125 10.135 10.211 11 | 1TSB H5 9 10.041 10.204 10.205 12 | 1TSB C6 10 10.172 10.103 10.340 13 | 1TSB H6 11 10.128 10.154 10.429 14 | 1TSB C7 12 10.130 10.085 9.964 15 | 1TSB H7 13 10.160 10.015 9.892 16 | 1TSB C8 14 10.013 10.153 9.938 17 | 1TSB H8 15 9.993 10.233 10.006 18 | 1TSB C9 16 9.911 10.115 9.847 19 | 1TSB C10 17 9.790 10.194 9.843 20 | 1TSB H10 18 9.779 10.285 9.892 21 | 1TSB C11 19 9.687 10.148 9.762 22 | 1TSB H11 20 9.595 10.206 9.766 23 | 1TSB C12 21 9.697 10.034 9.681 24 | 1TSB H12 22 9.615 10.009 9.612 25 | 1TSB C13 23 9.816 9.948 9.686 26 | 1TSB H13 24 9.828 9.857 9.627 27 | 1TSB C14 25 9.916 9.997 9.770 28 | 1TSB H14 26 10.008 9.933 9.771 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/eq_gro/md-equilb9.gro: -------------------------------------------------------------------------------- 1 | generated by VMD, t= 0.000000 2 | 26 3 | 1TSB C1 1 10.279 9.981 10.347 4 | 1TSB H1 2 10.322 9.963 10.450 5 | 1TSB C2 3 10.331 9.921 10.235 6 | 1TSB H2 4 10.409 9.843 10.242 7 | 1TSB C3 5 10.284 9.961 10.109 8 | 1TSB H3 6 10.315 9.925 10.018 9 | 1TSB C4 7 10.180 10.059 10.097 10 | 1TSB C5 8 10.130 10.119 10.208 11 | 1TSB H5 9 10.051 10.189 10.200 12 | 1TSB C6 10 10.184 10.082 10.336 13 | 1TSB H6 11 10.153 10.134 10.424 14 | 1TSB C7 12 10.131 10.091 9.963 15 | 1TSB H7 13 10.179 10.031 9.886 16 | 1TSB C8 14 10.012 10.162 9.937 17 | 1TSB H8 15 9.973 10.233 10.013 18 | 1TSB C9 16 9.914 10.107 9.850 19 | 1TSB C10 17 9.787 10.167 9.849 20 | 1TSB H10 18 9.770 10.253 9.907 21 | 1TSB C11 19 9.685 10.125 9.756 22 | 1TSB H11 20 9.592 10.184 9.752 23 | 1TSB C12 21 9.708 10.013 9.673 24 | 1TSB H12 22 9.627 9.975 9.611 25 | 1TSB C13 23 9.841 9.961 9.670 26 | 1TSB H13 24 9.856 9.888 9.591 27 | 1TSB C14 25 9.941 10.003 9.757 28 | 1TSB H14 26 10.032 9.950 9.740 29 | 20.00000 20.00000 20.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30 | -------------------------------------------------------------------------------- /stilbene_vacuum/index.ndx: -------------------------------------------------------------------------------- 1 | [ System ] 2 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 3 | 16 17 18 19 20 21 22 23 24 25 26 4 | [ Other ] 5 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 6 | 16 17 18 19 20 21 22 23 24 25 26 7 | [ TSB ] 8 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 9 | 16 17 18 19 20 21 22 23 24 25 26 10 | [ group1 ] 11 | 1 2 3 4 5 6 7 8 9 10 11 12 | [ group2 ] 13 | 12 14 | [ group3 ] 15 | 14 16 | [ group4 ] 17 | 16 17 18 19 20 21 22 23 24 25 26 18 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/profile-10ps.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 19:38:01 2020 2 | # Created by: 3 | # :-) GROMACS - gmx wham, 2022-dev-20201126-e550321ab1-unknown (double precision) (-: 4 | # 5 | # Executable: /scratch/project_2001312/gromacs_cp2k/build/bin/gmx 6 | # Data prefix: /scratch/project_2001312/gromacs_cp2k/gromacs (source tree) 7 | # Working dir: /scratch/project_2001312/Winter-School-2020/stilbene-vacuum/us-windows/profile 8 | # Command line: 9 | # gmx wham -it tpr-files.dat -ix pullx-files.dat -o -hist -unit kJ -min -180 -max 20 -b 0 -bins 50 10 | # gmx wham is part of G R O M A C S: 11 | # 12 | # S C A M O R G 13 | # 14 | @ title "Umbrella potential" 15 | @ xaxis label "\xx\f{} (deg)" 16 | @ yaxis label "E (kJ mol\S-1\N)" 17 | @TYPE xy 18 | -1.780000e+02 0.000000e+00 19 | -1.740000e+02 -4.357276e-02 20 | -1.700000e+02 1.313565e+00 21 | -1.660000e+02 3.030634e+00 22 | -1.620000e+02 4.573223e+00 23 | -1.580000e+02 6.694298e+00 24 | -1.540000e+02 9.675444e+00 25 | -1.500000e+02 1.278050e+01 26 | -1.460000e+02 1.469110e+01 27 | -1.420000e+02 1.854434e+01 28 | -1.380000e+02 2.290784e+01 29 | -1.340000e+02 2.767286e+01 30 | -1.300000e+02 3.232293e+01 31 | -1.260000e+02 3.807955e+01 32 | -1.220000e+02 4.461048e+01 33 | -1.180000e+02 5.136402e+01 34 | -1.140000e+02 5.812055e+01 35 | -1.100000e+02 6.436856e+01 36 | -1.060000e+02 7.132770e+01 37 | -1.020000e+02 7.902130e+01 38 | -9.800000e+01 8.581442e+01 39 | -9.400000e+01 9.173661e+01 40 | -9.000000e+01 9.965946e+01 41 | -8.600000e+01 1.082528e+02 42 | -8.200000e+01 9.956073e+01 43 | -7.800000e+01 9.248653e+01 44 | -7.400000e+01 8.669307e+01 45 | -7.000000e+01 8.089524e+01 46 | -6.600000e+01 7.523405e+01 47 | -6.200000e+01 7.092920e+01 48 | -5.800000e+01 6.698839e+01 49 | -5.400000e+01 6.294739e+01 50 | -5.000000e+01 5.876007e+01 51 | -4.600000e+01 5.520171e+01 52 | -4.200000e+01 5.245982e+01 53 | -3.800000e+01 4.987557e+01 54 | -3.400000e+01 4.758460e+01 55 | -3.000000e+01 4.550757e+01 56 | -2.600000e+01 4.383837e+01 57 | -2.200000e+01 4.263642e+01 58 | -1.800000e+01 4.185946e+01 59 | -1.400000e+01 4.107885e+01 60 | -1.000000e+01 4.090832e+01 61 | -6.000000e+00 4.174649e+01 62 | -2.000000e+00 4.154968e+01 63 | 2.000000e+00 4.130641e+01 64 | 6.000000e+00 4.189818e+01 65 | 1.000000e+01 4.341491e+01 66 | 1.400000e+01 4.513775e+01 67 | 1.800000e+01 4.589245e+01 68 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/profile.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Mon Nov 30 21:26:52 2020 2 | # Created by: 3 | # :-) GROMACS - gmx wham, 2022-dev-UNCHECKED (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/gmx 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/profile 8 | # Command line: 9 | # gmx wham -it tpr-files.dat -ix pullx-files.dat -o -hist -unit kJ -min -180 -max 20 -b 0 -bins 50 10 | # gmx wham is part of G R O M A C S: 11 | # 12 | # Getting the Right Output Means no Artefacts in Calculating Stuff 13 | # 14 | @ title "Umbrella potential" 15 | @ xaxis label "\xx\f{} (deg)" 16 | @ yaxis label "E (kJ mol\S-1\N)" 17 | @TYPE xy 18 | -1.780000e+02 0.000000e+00 19 | -1.740000e+02 -2.098944e+00 20 | -1.700000e+02 1.382373e+00 21 | -1.660000e+02 3.493535e+00 22 | -1.620000e+02 7.108763e+00 23 | -1.580000e+02 7.730959e+00 24 | -1.540000e+02 1.340338e+01 25 | -1.500000e+02 1.980463e+01 26 | -1.460000e+02 2.318250e+01 27 | -1.420000e+02 2.228640e+01 28 | -1.380000e+02 2.907365e+01 29 | -1.340000e+02 2.608592e+01 30 | -1.300000e+02 3.117268e+01 31 | -1.260000e+02 3.649215e+01 32 | -1.220000e+02 4.129953e+01 33 | -1.180000e+02 4.628125e+01 34 | -1.140000e+02 5.257056e+01 35 | -1.100000e+02 5.732679e+01 36 | -1.060000e+02 5.840167e+01 37 | -1.020000e+02 6.168096e+01 38 | -9.800000e+01 6.682797e+01 39 | -9.400000e+01 7.066908e+01 40 | -9.000000e+01 7.927347e+01 41 | -8.600000e+01 -4.791955e-01 42 | -8.200000e+01 7.843947e+01 43 | -7.800000e+01 7.426553e+01 44 | -7.400000e+01 6.708515e+01 45 | -7.000000e+01 6.394761e+01 46 | -6.600000e+01 5.811261e+01 47 | -6.200000e+01 5.074156e+01 48 | -5.800000e+01 4.496543e+01 49 | -5.400000e+01 4.007086e+01 50 | -5.000000e+01 3.385856e+01 51 | -4.600000e+01 2.824159e+01 52 | -4.200000e+01 2.590161e+01 53 | -3.800000e+01 2.299911e+01 54 | -3.400000e+01 2.053158e+01 55 | -3.000000e+01 1.827952e+01 56 | -2.600000e+01 1.633722e+01 57 | -2.200000e+01 1.317686e+01 58 | -1.800000e+01 1.038119e+01 59 | -1.400000e+01 8.793826e+00 60 | -1.000000e+01 8.928898e+00 61 | -6.000000e+00 9.062154e+00 62 | -2.000000e+00 9.894313e+00 63 | 2.000000e+00 9.251844e+00 64 | 6.000000e+00 9.106224e+00 65 | 1.000000e+01 1.081563e+01 66 | 1.400000e+01 1.157747e+01 67 | 1.800000e+01 1.180785e+01 68 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx-files.dat: -------------------------------------------------------------------------------- 1 | pullx1.xvg 2 | pullx10.xvg 3 | pullx11.xvg 4 | pullx12.xvg 5 | pullx13.xvg 6 | pullx14.xvg 7 | pullx15.xvg 8 | pullx16.xvg 9 | pullx17.xvg 10 | pullx18.xvg 11 | pullx19.xvg 12 | pullx2.xvg 13 | pullx20.xvg 14 | pullx21.xvg 15 | pullx22.xvg 16 | pullx23.xvg 17 | pullx24.xvg 18 | pullx25.xvg 19 | pullx26.xvg 20 | pullx27.xvg 21 | pullx28.xvg 22 | pullx29.xvg 23 | pullx3.xvg 24 | pullx30.xvg 25 | pullx4.xvg 26 | pullx5.xvg 27 | pullx6.xvg 28 | pullx7.xvg 29 | pullx8.xvg 30 | pullx9.xvg 31 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx1.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 16:53:28 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/1 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb1.tpr -deffnm md-equilb1 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 179.129 19 | 0.0010 179.124 20 | 0.0020 179.129 21 | 0.0030 179.141 22 | 0.0040 179.16 23 | 0.0050 179.183 24 | 0.0060 179.206 25 | 0.0070 179.225 26 | 0.0080 179.239 27 | 0.0090 179.245 28 | 0.0100 179.245 29 | 0.0110 179.239 30 | 0.0120 179.223 31 | 0.0130 179.194 32 | 0.0140 179.149 33 | 0.0150 179.082 34 | 0.0160 178.994 35 | 0.0170 178.886 36 | 0.0180 178.759 37 | 0.0190 178.615 38 | 0.0200 178.462 39 | 0.0210 178.299 40 | 0.0220 178.129 41 | 0.0230 177.955 42 | 0.0240 177.784 43 | 0.0250 177.622 44 | 0.0260 177.48 45 | 0.0270 177.364 46 | 0.0280 177.276 47 | 0.0290 177.22 48 | 0.0300 177.191 49 | 0.0310 177.185 50 | 0.0320 177.195 51 | 0.0330 177.221 52 | 0.0340 177.266 53 | 0.0350 177.338 54 | 0.0360 177.439 55 | 0.0370 177.569 56 | 0.0380 177.728 57 | 0.0390 177.909 58 | 0.0400 178.109 59 | 0.0410 178.321 60 | 0.0420 178.542 61 | 0.0430 178.767 62 | 0.0440 178.997 63 | 0.0450 179.232 64 | 0.0460 179.471 65 | 0.0470 179.708 66 | 0.0480 179.941 67 | 0.0490 -179.833 68 | 0.0500 -179.618 69 | 0.0510 -179.416 70 | 0.0520 -179.225 71 | 0.0530 -179.045 72 | 0.0540 -178.875 73 | 0.0550 -178.717 74 | 0.0560 -178.573 75 | 0.0570 -178.446 76 | 0.0580 -178.334 77 | 0.0590 -178.233 78 | 0.0600 -178.143 79 | 0.0610 -178.058 80 | 0.0620 -177.978 81 | 0.0630 -177.904 82 | 0.0640 -177.837 83 | 0.0650 -177.777 84 | 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21:57:05 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/11 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb11.tpr -deffnm md-equilb11 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # GRowing Old MAkes el Chrono Sweat 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -117.417 19 | 0.0010 -117.88 20 | 0.0020 -118.344 21 | 0.0030 -118.829 22 | 0.0040 -119.363 23 | 0.0050 -119.958 24 | 0.0060 -120.616 25 | 0.0070 -121.316 26 | 0.0080 -122.028 27 | 0.0090 -122.707 28 | 0.0100 -123.307 29 | 0.0110 -123.773 30 | 0.0120 -124.065 31 | 0.0130 -124.189 32 | 0.0140 -124.177 33 | 0.0150 -124.072 34 | 0.0160 -123.916 35 | 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| 0.0650 -119.245 84 | 0.0660 -119.475 85 | 0.0670 -119.495 86 | 0.0680 -119.336 87 | 0.0690 -119.054 88 | 0.0700 -118.708 89 | 0.0710 -118.349 90 | 0.0720 -118.019 91 | 0.0730 -117.749 92 | 0.0740 -117.545 93 | 0.0750 -117.388 94 | 0.0760 -117.239 95 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx12.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 22:27:25 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/12 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb12.tpr -deffnm md-equilb12 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gnomes, ROck Monsters And Chili Sauce 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -97.7998 19 | 0.0010 -98.0454 20 | 0.0020 -98.3528 21 | 0.0030 -98.691 22 | 0.0040 -99.02 23 | 0.0050 -99.3176 24 | 0.0060 -99.5902 25 | 0.0070 -99.8617 26 | 0.0080 -100.141 27 | 0.0090 -100.419 28 | 0.0100 -100.686 29 | 0.0110 -100.943 30 | 0.0120 -101.201 31 | 0.0130 -101.466 32 | 0.0140 -101.728 33 | 0.0150 -101.966 34 | 0.0160 -102.175 35 | 0.0170 -102.374 36 | 0.0180 -102.591 37 | 0.0190 -102.84 38 | 0.0200 -103.108 39 | 0.0210 -103.379 40 | 0.0220 -103.637 41 | 0.0230 -103.875 42 | 0.0240 -104.081 43 | 0.0250 -104.231 44 | 0.0260 -104.305 45 | 0.0270 -104.322 46 | 0.0280 -104.328 47 | 0.0290 -104.365 48 | 0.0300 -104.452 49 | 0.0310 -104.581 50 | 0.0320 -104.742 51 | 0.0330 -104.928 52 | 0.0340 -105.134 53 | 0.0350 -105.34 54 | 0.0360 -105.516 55 | 0.0370 -105.634 56 | 0.0380 -105.69 57 | 0.0390 -105.697 58 | 0.0400 -105.663 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-111.336 107 | 0.0890 -112.026 108 | 0.0900 -112.535 109 | 0.0910 -112.805 110 | 0.0920 -112.84 111 | 0.0930 -112.691 112 | 0.0940 -112.407 113 | 0.0950 -112.032 114 | 0.0960 -111.611 115 | 0.0970 -111.197 116 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx13.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 22:57:45 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/13 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb13.tpr -deffnm md-equilb13 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gnomes, ROck Monsters And Chili Sauce 13 | # 14 | @ 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61 | 0.0430 -119.088 62 | 0.0440 -119.13 63 | 0.0450 -119.096 64 | 0.0460 -119.003 65 | 0.0470 -118.866 66 | 0.0480 -118.695 67 | 0.0490 -118.496 68 | 0.0500 -118.279 69 | 0.0510 -118.049 70 | 0.0520 -117.809 71 | 0.0530 -117.548 72 | 0.0540 -117.257 73 | 0.0550 -116.918 74 | 0.0560 -116.517 75 | 0.0570 -116.038 76 | 0.0580 -115.465 77 | 0.0590 -114.786 78 | 0.0600 -114.005 79 | 0.0610 -113.149 80 | 0.0620 -112.26 81 | 0.0630 -111.398 82 | 0.0640 -110.609 83 | 0.0650 -109.922 84 | 0.0660 -109.38 85 | 0.0670 -109.019 86 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx14.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 23:28:05 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/14 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb14.tpr -deffnm md-equilb14 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -90.9209 19 | 0.0010 -91.5432 20 | 0.0020 -92.432 21 | 0.0030 -93.5341 22 | 0.0040 -94.7783 23 | 0.0050 -96.0772 24 | 0.0060 -97.3642 25 | 0.0070 -98.5763 26 | 0.0080 -99.6832 27 | 0.0090 -100.667 28 | 0.0100 -101.525 29 | 0.0110 -102.258 30 | 0.0120 -102.87 31 | 0.0130 -103.351 32 | 0.0140 -103.692 33 | 0.0150 -103.875 34 | 0.0160 -103.885 35 | 0.0170 -103.717 36 | 0.0180 -103.369 37 | 0.0190 -102.844 38 | 0.0200 -102.157 39 | 0.0210 -101.338 40 | 0.0220 -100.423 41 | 0.0230 -99.4504 42 | 0.0240 -98.4609 43 | 0.0250 -97.492 44 | 0.0260 -96.5572 45 | 0.0270 -95.6758 46 | 0.0280 -94.8746 47 | 0.0290 -94.1786 48 | 0.0300 -93.6182 49 | 0.0310 -93.2328 50 | 0.0320 -93.058 51 | 0.0330 -93.1171 52 | 0.0340 -93.4068 53 | 0.0350 -93.895 54 | 0.0360 -94.528 55 | 0.0370 -95.2429 56 | 0.0380 -95.9866 57 | 0.0390 -96.7087 58 | 0.0400 -97.374 59 | 0.0410 -97.9696 60 | 0.0420 -98.5009 61 | 0.0430 -98.997 62 | 0.0440 -99.4748 63 | 0.0450 -99.9459 64 | 0.0460 -100.406 65 | 0.0470 -100.839 66 | 0.0480 -101.226 67 | 0.0490 -101.543 68 | 0.0500 -101.776 69 | 0.0510 -101.921 70 | 0.0520 -101.989 71 | 0.0530 -102.003 72 | 0.0540 -101.997 73 | 0.0550 -102 74 | 0.0560 -102.025 75 | 0.0570 -102.065 76 | 0.0580 -102.099 77 | 0.0590 -102.095 78 | 0.0600 -102.022 79 | 0.0610 -101.86 80 | 0.0620 -101.6 81 | 0.0630 -101.25 82 | 0.0640 -100.831 83 | 0.0650 -100.376 84 | 0.0660 -99.9093 85 | 0.0670 -99.4404 86 | 0.0680 -98.9683 87 | 0.0690 -98.4796 88 | 0.0700 -97.9477 89 | 0.0710 -97.351 90 | 0.0720 -96.6731 91 | 0.0730 -95.9105 92 | 0.0740 -95.092 93 | 0.0750 -94.2814 94 | 0.0760 -93.5313 95 | 0.0770 -92.9052 96 | 0.0780 -92.4483 97 | 0.0790 -92.1789 98 | 0.0800 -92.0858 99 | 0.0810 -92.1418 100 | 0.0820 -92.3109 101 | 0.0830 -92.5641 102 | 0.0840 -92.89 103 | 0.0850 -93.3006 104 | 0.0860 -93.8173 105 | 0.0870 -94.4626 106 | 0.0880 -95.2271 107 | 0.0890 -96.0859 108 | 0.0900 -96.9838 109 | 0.0910 -97.8536 110 | 0.0920 -98.6201 111 | 0.0930 -99.2373 112 | 0.0940 -99.6832 113 | 0.0950 -99.9569 114 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx15.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 23:58:25 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/15 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb15.tpr -deffnm md-equilb15 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Good ROcking Metal Altar for Chronical Sinners 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -78.2187 19 | 0.0010 -78.3692 20 | 0.0020 -78.2399 21 | 0.0030 -77.8244 22 | 0.0040 -77.1174 23 | 0.0050 -76.1221 24 | 0.0060 -74.8417 25 | 0.0070 -73.3067 26 | 0.0080 -71.5489 27 | 0.0090 -69.6194 28 | 0.0100 -67.5824 29 | 0.0110 -65.5024 30 | 0.0120 -63.4177 31 | 0.0130 -61.395 32 | 0.0140 -59.4948 33 | 0.0150 -57.8007 34 | 0.0160 -56.3636 35 | 0.0170 -55.2551 36 | 0.0180 -54.5361 37 | 0.0190 -54.2511 38 | 0.0200 -54.4137 39 | 0.0210 -55.0065 40 | 0.0220 -55.9804 41 | 0.0230 -57.2828 42 | 0.0240 -58.8357 43 | 0.0250 -60.5454 44 | 0.0260 -62.3312 45 | 0.0270 -64.1013 46 | 0.0280 -65.7838 47 | 0.0290 -67.3296 48 | 0.0300 -68.7028 49 | 0.0310 -69.9099 50 | 0.0320 -70.9607 51 | 0.0330 -71.8658 52 | 0.0340 -72.6394 53 | 0.0350 -73.2828 54 | 0.0360 -73.7973 55 | 0.0370 -74.18 56 | 0.0380 -74.4312 57 | 0.0390 -74.5677 58 | 0.0400 -74.6084 59 | 0.0410 -74.5785 60 | 0.0420 -74.5033 61 | 0.0430 -74.4022 62 | 0.0440 -74.2837 63 | 0.0450 -74.1462 64 | 0.0460 -73.9872 65 | 0.0470 -73.8139 66 | 0.0480 -73.6462 67 | 0.0490 -73.5071 68 | 0.0500 -73.416 69 | 0.0510 -73.3835 70 | 0.0520 -73.41 71 | 0.0530 -73.4872 72 | 0.0540 -73.5985 73 | 0.0550 -73.7202 74 | 0.0560 -73.8299 75 | 0.0570 -73.9064 76 | 0.0580 -73.9305 77 | 0.0590 -73.8815 78 | 0.0600 -73.7363 79 | 0.0610 -73.4725 80 | 0.0620 -73.0775 81 | 0.0630 -72.545 82 | 0.0640 -71.8792 83 | 0.0650 -71.0992 84 | 0.0660 -70.2325 85 | 0.0670 -69.3182 86 | 0.0680 -68.4025 87 | 0.0690 -67.5206 88 | 0.0700 -66.6954 89 | 0.0710 -65.942 90 | 0.0720 -65.275 91 | 0.0730 -64.7113 92 | 0.0740 -64.2707 93 | 0.0750 -63.9744 94 | 0.0760 -63.8473 95 | 0.0770 -63.9236 96 | 0.0780 -64.2428 97 | 0.0790 -64.832 98 | 0.0800 -65.6954 99 | 0.0810 -66.7985 100 | 0.0820 -68.1008 101 | 0.0830 -69.547 102 | 0.0840 -71.0748 103 | 0.0850 -72.6341 104 | 0.0860 -74.1892 105 | 0.0870 -75.718 106 | 0.0880 -77.2 107 | 0.0890 -78.5955 108 | 0.0900 -79.8716 109 | 0.0910 -80.9774 110 | 0.0920 -81.8809 111 | 0.0930 -82.5753 112 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx16.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 00:28:48 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/16 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb16.tpr -deffnm md-equilb16 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # GRowing Old MAkes el Chrono Sweat 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -75.6568 19 | 0.0010 -75.5328 20 | 0.0020 -75.1821 21 | 0.0030 -74.5929 22 | 0.0040 -73.7578 23 | 0.0050 -72.6842 24 | 0.0060 -71.3804 25 | 0.0070 -69.8747 26 | 0.0080 -68.2007 27 | 0.0090 -66.375 28 | 0.0100 -64.4455 29 | 0.0110 -62.4769 30 | 0.0120 -60.5272 31 | 0.0130 -58.6442 32 | 0.0140 -56.8835 33 | 0.0150 -55.276 34 | 0.0160 -53.8947 35 | 0.0170 -52.7662 36 | 0.0180 -51.9214 37 | 0.0190 -51.3751 38 | 0.0200 -51.1215 39 | 0.0210 -51.1597 40 | 0.0220 -51.4771 41 | 0.0230 -52.0527 42 | 0.0240 -52.8495 43 | 0.0250 -53.8267 44 | 0.0260 -54.9218 45 | 0.0270 -56.051 46 | 0.0280 -57.1581 47 | 0.0290 -58.1968 48 | 0.0300 -59.135 49 | 0.0310 -59.9739 50 | 0.0320 -60.7161 51 | 0.0330 -61.3855 52 | 0.0340 -61.9853 53 | 0.0350 -62.5142 54 | 0.0360 -62.9745 55 | 0.0370 -63.3659 56 | 0.0380 -63.6872 57 | 0.0390 -63.9522 58 | 0.0400 -64.1825 59 | 0.0410 -64.3995 60 | 0.0420 -64.6238 61 | 0.0430 -64.8748 62 | 0.0440 -65.1632 63 | 0.0450 -65.4969 64 | 0.0460 -65.8835 65 | 0.0470 -66.3339 66 | 0.0480 -66.8507 67 | 0.0490 -67.4324 68 | 0.0500 -68.0713 69 | 0.0510 -68.75 70 | 0.0520 -69.4479 71 | 0.0530 -70.1479 72 | 0.0540 -70.8248 73 | 0.0550 -71.4629 74 | 0.0560 -72.0373 75 | 0.0570 -72.525 76 | 0.0580 -72.8951 77 | 0.0590 -73.1142 78 | 0.0600 -73.1461 79 | 0.0610 -72.9652 80 | 0.0620 -72.5583 81 | 0.0630 -71.9336 82 | 0.0640 -71.1138 83 | 0.0650 -70.131 84 | 0.0660 -69.0181 85 | 0.0670 -67.8137 86 | 0.0680 -66.5356 87 | 0.0690 -65.2016 88 | 0.0700 -63.8206 89 | 0.0710 -62.4171 90 | 0.0720 -61.0434 91 | 0.0730 -59.759 92 | 0.0740 -58.642 93 | 0.0750 -57.7537 94 | 0.0760 -57.1476 95 | 0.0770 -56.8663 96 | 0.0780 -56.9334 97 | 0.0790 -57.3583 98 | 0.0800 -58.1331 99 | 0.0810 -59.2362 100 | 0.0820 -60.637 101 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx17.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 00:59:10 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/17 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb17.tpr -deffnm md-equilb17 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gravel Rubs Often Many Awfully Cauterized Sores 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -64.0261 19 | 0.0010 -63.9808 20 | 0.0020 -63.7186 21 | 0.0030 -63.256 22 | 0.0040 -62.6118 23 | 0.0050 -61.7956 24 | 0.0060 -60.8184 25 | 0.0070 -59.6756 26 | 0.0080 -58.3751 27 | 0.0090 -56.9397 28 | 0.0100 -55.3959 29 | 0.0110 -53.7794 30 | 0.0120 -52.1535 31 | 0.0130 -50.5691 32 | 0.0140 -49.0845 33 | 0.0150 -47.7409 34 | 0.0160 -46.5782 35 | 0.0170 -45.6166 36 | 0.0180 -44.8757 37 | 0.0190 -44.3652 38 | 0.0200 -44.0803 39 | 0.0210 -44.0178 40 | 0.0220 -44.1678 41 | 0.0230 -44.5219 42 | 0.0240 -45.0707 43 | 0.0250 -45.8089 44 | 0.0260 -46.7223 45 | 0.0270 -47.7849 46 | 0.0280 -48.9513 47 | 0.0290 -50.1834 48 | 0.0300 -51.4309 49 | 0.0310 -52.666 50 | 0.0320 -53.8648 51 | 0.0330 -54.995 52 | 0.0340 -56.0467 53 | 0.0350 -57.0314 54 | 0.0360 -57.9467 55 | 0.0370 -58.785 56 | 0.0380 -59.5353 57 | 0.0390 -60.1805 58 | 0.0400 -60.7107 59 | 0.0410 -61.1252 60 | 0.0420 -61.4317 61 | 0.0430 -61.6433 62 | 0.0440 -61.7746 63 | 0.0450 -61.8416 64 | 0.0460 -61.8595 65 | 0.0470 -61.8415 66 | 0.0480 -61.7999 67 | 0.0490 -61.7438 68 | 0.0500 -61.6801 69 | 0.0510 -61.612 70 | 0.0520 -61.5399 71 | 0.0530 -61.4612 72 | 0.0540 -61.3716 73 | 0.0550 -61.2671 74 | 0.0560 -61.1468 75 | 0.0570 -61.0125 76 | 0.0580 -60.8698 77 | 0.0590 -60.7222 78 | 0.0600 -60.5635 79 | 0.0610 -60.3811 80 | 0.0620 -60.1617 81 | 0.0630 -59.8995 82 | 0.0640 -59.5947 83 | 0.0650 -59.2609 84 | 0.0660 -58.9188 85 | 0.0670 -58.6049 86 | 0.0680 -58.352 87 | 0.0690 -58.1792 88 | 0.0700 -58.0815 89 | 0.0710 -58.0377 90 | 0.0720 -58.0246 91 | 0.0730 -58.0298 92 | 0.0740 -58.0522 93 | 0.0750 -58.1017 94 | 0.0760 -58.197 95 | 0.0770 -58.3628 96 | 0.0780 -58.6215 97 | 0.0790 -58.9866 98 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx18.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 01:29:31 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/18 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb18.tpr -deffnm md-equilb18 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # God Rules Over Mankind, Animals, Cosmos and Such 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -56.0572 19 | 0.0010 -55.8602 20 | 0.0020 -55.5634 21 | 0.0030 -55.1708 22 | 0.0040 -54.6952 23 | 0.0050 -54.1565 24 | 0.0060 -53.5689 25 | 0.0070 -52.9478 26 | 0.0080 -52.3204 27 | 0.0090 -51.7045 28 | 0.0100 -51.1095 29 | 0.0110 -50.5598 30 | 0.0120 -50.0583 31 | 0.0130 -49.6037 32 | 0.0140 -49.1991 33 | 0.0150 -48.8358 34 | 0.0160 -48.5082 35 | 0.0170 -48.213 36 | 0.0180 -47.9487 37 | 0.0190 -47.7146 38 | 0.0200 -47.5099 39 | 0.0210 -47.3284 40 | 0.0220 -47.1597 41 | 0.0230 -46.9828 42 | 0.0240 -46.7804 43 | 0.0250 -46.5429 44 | 0.0260 -46.2685 45 | 0.0270 -45.9705 46 | 0.0280 -45.6646 47 | 0.0290 -45.3722 48 | 0.0300 -45.1182 49 | 0.0310 -44.9221 50 | 0.0320 -44.797 51 | 0.0330 -44.7432 52 | 0.0340 -44.7519 53 | 0.0350 -44.8141 54 | 0.0360 -44.9265 55 | 0.0370 -45.0907 56 | 0.0380 -45.3139 57 | 0.0390 -45.6057 58 | 0.0400 -45.9821 59 | 0.0410 -46.4644 60 | 0.0420 -47.0777 61 | 0.0430 -47.8337 62 | 0.0440 -48.7222 63 | 0.0450 -49.7087 64 | 0.0460 -50.7609 65 | 0.0470 -51.8249 66 | 0.0480 -52.879 67 | 0.0490 -53.913 68 | 0.0500 -54.9076 69 | 0.0510 -55.8815 70 | 0.0520 -56.8453 71 | 0.0530 -57.8073 72 | 0.0540 -58.7443 73 | 0.0550 -59.6221 74 | 0.0560 -60.3797 75 | 0.0570 -60.9594 76 | 0.0580 -61.3151 77 | 0.0590 -61.4153 78 | 0.0600 -61.2468 79 | 0.0610 -60.8156 80 | 0.0620 -60.1399 81 | 0.0630 -59.2426 82 | 0.0640 -58.1459 83 | 0.0650 -56.8679 84 | 0.0660 -55.4516 85 | 0.0670 -53.9096 86 | 0.0680 -52.2794 87 | 0.0690 -50.6245 88 | 0.0700 -48.9847 89 | 0.0710 -47.4062 90 | 0.0720 -45.9395 91 | 0.0730 -44.6164 92 | 0.0740 -43.4508 93 | 0.0750 -42.4667 94 | 0.0760 -41.6911 95 | 0.0770 -41.1571 96 | 0.0780 -40.8927 97 | 0.0790 -40.9178 98 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx19.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 01:59:53 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/19 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb19.tpr -deffnm md-equilb19 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Good gRace! Old Maple Actually Chews Slate 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -44.9528 19 | 0.0010 -45.0787 20 | 0.0020 -45.1579 21 | 0.0030 -45.1766 22 | 0.0040 -45.1235 23 | 0.0050 -44.9904 24 | 0.0060 -44.7729 25 | 0.0070 -44.4723 26 | 0.0080 -44.0908 27 | 0.0090 -43.644 28 | 0.0100 -43.1524 29 | 0.0110 -42.6312 30 | 0.0120 -42.1014 31 | 0.0130 -41.5719 32 | 0.0140 -41.0457 33 | 0.0150 -40.5218 34 | 0.0160 -40.0035 35 | 0.0170 -39.5135 36 | 0.0180 -39.0642 37 | 0.0190 -38.6825 38 | 0.0200 -38.4006 39 | 0.0210 -38.2508 40 | 0.0220 -38.2701 41 | 0.0230 -38.4839 42 | 0.0240 -38.8925 43 | 0.0250 -39.4714 44 | 0.0260 -40.1853 45 | 0.0270 -40.9951 46 | 0.0280 -41.8731 47 | 0.0290 -42.7897 48 | 0.0300 -43.6987 49 | 0.0310 -44.5877 50 | 0.0320 -45.4502 51 | 0.0330 -46.2979 52 | 0.0340 -47.1258 53 | 0.0350 -47.9241 54 | 0.0360 -48.6557 55 | 0.0370 -49.2907 56 | 0.0380 -49.8294 57 | 0.0390 -50.2637 58 | 0.0400 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| -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx2.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 17:23:48 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/2 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb2.tpr -deffnm md-equilb2 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gnomes, ROck Monsters And Chili Sauce 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -171.953 19 | 0.0010 -172.299 20 | 0.0020 -172.652 21 | 0.0030 -173.004 22 | 0.0040 -173.343 23 | 0.0050 -173.664 24 | 0.0060 -173.963 25 | 0.0070 -174.238 26 | 0.0080 -174.489 27 | 0.0090 -174.713 28 | 0.0100 -174.911 29 | 0.0110 -175.084 30 | 0.0120 -175.231 31 | 0.0130 -175.348 32 | 0.0140 -175.435 33 | 0.0150 -175.494 34 | 0.0160 -175.531 35 | 0.0170 -175.555 36 | 0.0180 -175.573 37 | 0.0190 -175.592 38 | 0.0200 -175.613 39 | 0.0210 -175.636 40 | 0.0220 -175.658 41 | 0.0230 -175.676 42 | 0.0240 -175.689 43 | 0.0250 -175.697 44 | 0.0260 -175.706 45 | 0.0270 -175.72 46 | 0.0280 -175.742 47 | 0.0290 -175.771 48 | 0.0300 -175.806 49 | 0.0310 -175.841 50 | 0.0320 -175.873 51 | 0.0330 -175.897 52 | 0.0340 -175.913 53 | 0.0350 -175.919 54 | 0.0360 -175.915 55 | 0.0370 -175.9 56 | 0.0380 -175.873 57 | 0.0390 -175.832 58 | 0.0400 -175.778 59 | 0.0410 -175.711 60 | 0.0420 -175.633 61 | 0.0430 -175.547 62 | 0.0440 -175.453 63 | 0.0450 -175.351 64 | 0.0460 -175.236 65 | 0.0470 -175.104 66 | 0.0480 -174.956 67 | 0.0490 -174.795 68 | 0.0500 -174.626 69 | 0.0510 -174.45 70 | 0.0520 -174.271 71 | 0.0530 -174.089 72 | 0.0540 -173.906 73 | 0.0550 -173.717 74 | 0.0560 -173.518 75 | 0.0570 -173.305 76 | 0.0580 -173.079 77 | 0.0590 -172.85 78 | 0.0600 -172.622 79 | 0.0610 -172.404 80 | 0.0620 -172.201 81 | 0.0630 -172.008 82 | 0.0640 -171.822 83 | 0.0650 -171.637 84 | 0.0660 -171.446 85 | 0.0670 -171.244 86 | 0.0680 -171.028 87 | 0.0690 -170.8 88 | 0.0700 -170.564 89 | 0.0710 -170.324 90 | 0.0720 -170.08 91 | 0.0730 -169.835 92 | 0.0740 -169.583 93 | 0.0750 -169.326 94 | 0.0760 -169.068 95 | 0.0770 -168.813 96 | 0.0780 -168.561 97 | 0.0790 -168.322 98 | 0.0800 -168.099 99 | 0.0810 -167.905 100 | 0.0820 -167.75 101 | 0.0830 -167.641 102 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx20.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 02:30:17 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/20 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb20.tpr -deffnm md-equilb20 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # God Rules Over Mankind, Animals, Cosmos and Such 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -56.47 19 | 0.0010 -56.1119 20 | 0.0020 -55.5074 21 | 0.0030 -54.6532 22 | 0.0040 -53.5613 23 | 0.0050 -52.2558 24 | 0.0060 -50.7532 25 | 0.0070 -49.1131 26 | 0.0080 -47.3729 27 | 0.0090 -45.5906 28 | 0.0100 -43.827 29 | 0.0110 -42.1009 30 | 0.0120 -40.4857 31 | 0.0130 -39.0259 32 | 0.0140 -37.7791 33 | 0.0150 -36.8154 34 | 0.0160 -36.1793 35 | 0.0170 -35.9036 36 | 0.0180 -35.9831 37 | 0.0190 -36.3841 38 | 0.0200 -37.0573 39 | 0.0210 -37.9456 40 | 0.0220 -38.9751 41 | 0.0230 -40.0861 42 | 0.0240 -41.1974 43 | 0.0250 -42.2515 44 | 0.0260 -43.1687 45 | 0.0270 -43.887 46 | 0.0280 -44.3511 47 | 0.0290 -44.5393 48 | 0.0300 -44.4541 49 | 0.0310 -44.1181 50 | 0.0320 -43.5712 51 | 0.0330 -42.854 52 | 0.0340 -42.0032 53 | 0.0350 -41.0426 54 | 0.0360 -40.0079 55 | 0.0370 -38.9385 56 | 0.0380 -37.9074 57 | 0.0390 -36.9724 58 | 0.0400 -36.1977 59 | 0.0410 -35.6407 60 | 0.0420 -35.3409 61 | 0.0430 -35.3135 62 | 0.0440 -35.5648 63 | 0.0450 -36.0971 64 | 0.0460 -36.9127 65 | 0.0470 -37.9939 66 | 0.0480 -39.3281 67 | 0.0490 -40.887 68 | 0.0500 -42.5899 69 | 0.0510 -44.3567 70 | 0.0520 -46.1308 71 | 0.0530 -47.7955 72 | 0.0540 -49.2878 73 | 0.0550 -50.5524 74 | 0.0560 -51.5334 75 | 0.0570 -52.1706 76 | 0.0580 -52.4219 77 | 0.0590 -52.2714 78 | 0.0600 -51.7116 79 | 0.0610 -50.7576 80 | 0.0620 -49.4415 81 | 0.0630 -47.829 82 | 0.0640 -45.9735 83 | 0.0650 -43.9549 84 | 0.0660 -41.8078 85 | 0.0670 -39.6045 86 | 0.0680 -37.419 87 | 0.0690 -35.3262 88 | 0.0700 -33.3987 89 | 0.0710 -31.7414 90 | 0.0720 -30.4472 91 | 0.0730 -29.5778 92 | 0.0740 -29.1827 93 | 0.0750 -29.3007 94 | 0.0760 -29.9283 95 | 0.0770 -31.0358 96 | 0.0780 -32.5782 97 | 0.0790 -34.4587 98 | 0.0800 -36.596 99 | 0.0810 -38.886 100 | 0.0820 -41.208 101 | 0.0830 -43.4539 102 | 0.0840 -45.5409 103 | 0.0850 -47.4251 104 | 0.0860 -49.0764 105 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx21.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 03:00:44 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/21 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb21.tpr -deffnm md-equilb21 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # GROningen MAchine for Chemical Simulation 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -45.5037 19 | 0.0010 -45.0586 20 | 0.0020 -44.3199 21 | 0.0030 -43.3167 22 | 0.0040 -42.1058 23 | 0.0050 -40.752 24 | 0.0060 -39.3136 25 | 0.0070 -37.8606 26 | 0.0080 -36.4598 27 | 0.0090 -35.1762 28 | 0.0100 -34.0777 29 | 0.0110 -33.1968 30 | 0.0120 -32.5743 31 | 0.0130 -32.2144 32 | 0.0140 -32.1144 33 | 0.0150 -32.2585 34 | 0.0160 -32.6242 35 | 0.0170 -33.1856 36 | 0.0180 -33.9071 37 | 0.0190 -34.7471 38 | 0.0200 -35.6608 39 | 0.0210 -36.5885 40 | 0.0220 -37.4719 41 | 0.0230 -38.2297 42 | 0.0240 -38.8167 43 | 0.0250 -39.1821 44 | 0.0260 -39.3063 45 | 0.0270 -39.1842 46 | 0.0280 -38.8293 47 | 0.0290 -38.2637 48 | 0.0300 -37.5184 49 | 0.0310 -36.6203 50 | 0.0320 -35.6082 51 | 0.0330 -34.5299 52 | 0.0340 -33.4266 53 | 0.0350 -32.3405 54 | 0.0360 -31.3171 55 | 0.0370 -30.3988 56 | 0.0380 -29.6275 57 | 0.0390 -29.0266 58 | 0.0400 -28.6244 59 | 0.0410 -28.4468 60 | 0.0420 -28.5131 61 | 0.0430 -28.8365 62 | 0.0440 -29.4175 63 | 0.0450 -30.2309 64 | 0.0460 -31.2397 65 | 0.0470 -32.3921 66 | 0.0480 -33.6379 67 | 0.0490 -34.9098 68 | 0.0500 -36.1571 69 | 0.0510 -37.3355 70 | 0.0520 -38.4121 71 | 0.0530 -39.3472 72 | 0.0540 -40.1062 73 | 0.0550 -40.6586 74 | 0.0560 -40.9898 75 | 0.0570 -41.0926 76 | 0.0580 -40.9696 77 | 0.0590 -40.6277 78 | 0.0600 -40.0781 79 | 0.0610 -39.3237 80 | 0.0620 -38.3538 81 | 0.0630 -37.178 82 | 0.0640 -35.8136 83 | 0.0650 -34.3141 84 | 0.0660 -32.7288 85 | 0.0670 -31.1531 86 | 0.0680 -29.6869 87 | 0.0690 -28.4256 88 | 0.0700 -27.4365 89 | 0.0710 -26.7727 90 | 0.0720 -26.4696 91 | 0.0730 -26.5407 92 | 0.0740 -26.9801 93 | 0.0750 -27.7699 94 | 0.0760 -28.8687 95 | 0.0770 -30.2282 96 | 0.0780 -31.7836 97 | 0.0790 -33.4758 98 | 0.0800 -35.2635 99 | 0.0810 -37.0762 100 | 0.0820 -38.8824 101 | 0.0830 -40.6277 102 | 0.0840 -42.2435 103 | 0.0850 -43.6923 104 | 0.0860 -44.9032 105 | 0.0870 -45.8252 106 | 0.0880 -46.4273 107 | 0.0890 -46.6862 108 | 0.0900 -46.5936 109 | 0.0910 -46.1582 110 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx22.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 03:31:08 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/22 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb22.tpr -deffnm md-equilb22 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gyas ROwers Mature At Cryogenic Speed 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -36.7223 19 | 0.0010 -36.6596 20 | 0.0020 -36.3292 21 | 0.0030 -35.7144 22 | 0.0040 -34.8158 23 | 0.0050 -33.6527 24 | 0.0060 -32.2723 25 | 0.0070 -30.7307 26 | 0.0080 -29.123 27 | 0.0090 -27.5154 28 | 0.0100 -26.0016 29 | 0.0110 -24.6542 30 | 0.0120 -23.5277 31 | 0.0130 -22.6797 32 | 0.0140 -22.1306 33 | 0.0150 -21.8923 34 | 0.0160 -21.9565 35 | 0.0170 -22.2986 36 | 0.0180 -22.8846 37 | 0.0190 -23.6772 38 | 0.0200 -24.6463 39 | 0.0210 -25.7678 40 | 0.0220 -27.0123 41 | 0.0230 -28.306 42 | 0.0240 -29.579 43 | 0.0250 -30.7528 44 | 0.0260 -31.7511 45 | 0.0270 -32.5063 46 | 0.0280 -32.9847 47 | 0.0290 -33.1764 48 | 0.0300 -33.1039 49 | 0.0310 -32.8217 50 | 0.0320 -32.3895 51 | 0.0330 -31.848 52 | 0.0340 -31.228 53 | 0.0350 -30.557 54 | 0.0360 -29.8666 55 | 0.0370 -29.2091 56 | 0.0380 -28.6167 57 | 0.0390 -28.1175 58 | 0.0400 -27.7389 59 | 0.0410 -27.4986 60 | 0.0420 -27.4184 61 | 0.0430 -27.5074 62 | 0.0440 -27.7728 63 | 0.0450 -28.2185 64 | 0.0460 -28.8418 65 | 0.0470 -29.6277 66 | 0.0480 -30.5379 67 | 0.0490 -31.5299 68 | 0.0500 -32.5455 69 | 0.0510 -33.5255 70 | 0.0520 -34.4082 71 | 0.0530 -35.1635 72 | 0.0540 -35.7541 73 | 0.0550 -36.1473 74 | 0.0560 -36.3186 75 | 0.0570 -36.2449 76 | 0.0580 -35.9162 77 | 0.0590 -35.3308 78 | 0.0600 -34.5052 79 | 0.0610 -33.4631 80 | 0.0620 -32.233 81 | 0.0630 -30.8591 82 | 0.0640 -29.3798 83 | 0.0650 -27.858 84 | 0.0660 -26.344 85 | 0.0670 -24.8862 86 | 0.0680 -23.5382 87 | 0.0690 -22.3916 88 | 0.0700 -21.522 89 | 0.0710 -20.9873 90 | 0.0720 -20.8213 91 | 0.0730 -21.0283 92 | 0.0740 -21.5977 93 | 0.0750 -22.4979 94 | 0.0760 -23.6807 95 | 0.0770 -25.0931 96 | 0.0780 -26.6621 97 | 0.0790 -28.322 98 | 0.0800 -30.0053 99 | 0.0810 -31.654 100 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx23.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 04:01:26 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/23 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb23.tpr -deffnm md-equilb23 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gromacs Runs One Microsecond At Cannonball Speeds 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -32.5188 19 | 0.0010 -31.2037 20 | 0.0020 -29.6336 21 | 0.0030 -27.8709 22 | 0.0040 -26.004 23 | 0.0050 -24.1076 24 | 0.0060 -22.262 25 | 0.0070 -20.5181 26 | 0.0080 -18.9279 27 | 0.0090 -17.5254 28 | 0.0100 -16.3369 29 | 0.0110 -15.4068 30 | 0.0120 -14.7682 31 | 0.0130 -14.4395 32 | 0.0140 -14.4232 33 | 0.0150 -14.7011 34 | 0.0160 -15.2289 35 | 0.0170 -15.9475 36 | 0.0180 -16.7933 37 | 0.0190 -17.711 38 | 0.0200 -18.6613 39 | 0.0210 -19.6064 40 | 0.0220 -20.5001 41 | 0.0230 -21.2854 42 | 0.0240 -21.9131 43 | 0.0250 -22.3497 44 | 0.0260 -22.5698 45 | 0.0270 -22.5757 46 | 0.0280 -22.3854 47 | 0.0290 -22.0287 48 | 0.0300 -21.5422 49 | 0.0310 -20.9639 50 | 0.0320 -20.3246 51 | 0.0330 -19.6548 52 | 0.0340 -18.9863 53 | 0.0350 -18.3617 54 | 0.0360 -17.8229 55 | 0.0370 -17.4163 56 | 0.0380 -17.1673 57 | 0.0390 -17.0912 58 | 0.0400 -17.1864 59 | 0.0410 -17.4457 60 | 0.0420 -17.8616 61 | 0.0430 -18.4306 62 | 0.0440 -19.1532 63 | 0.0450 -20.0067 64 | 0.0460 -20.9703 65 | 0.0470 -22.0012 66 | 0.0480 -23.0702 67 | 0.0490 -24.1115 68 | 0.0500 -25.0929 69 | 0.0510 -25.9808 70 | 0.0520 -26.7357 71 | 0.0530 -27.3161 72 | 0.0540 -27.6843 73 | 0.0550 -27.7991 74 | 0.0560 -27.625 75 | 0.0570 -27.1448 76 | 0.0580 -26.3566 77 | 0.0590 -25.2942 78 | 0.0600 -24.0005 79 | 0.0610 -22.5404 80 | 0.0620 -20.9683 81 | 0.0630 -19.3468 82 | 0.0640 -17.7124 83 | 0.0650 -16.1102 84 | 0.0660 -14.6086 85 | 0.0670 -13.2768 86 | 0.0680 -12.174 87 | 0.0690 -11.3291 88 | 0.0700 -10.7925 89 | 0.0710 -10.5824 90 | 0.0720 -10.706 91 | 0.0730 -11.1567 92 | 0.0740 -11.9234 93 | 0.0750 -12.9952 94 | 0.0760 -14.342 95 | 0.0770 -15.9136 96 | 0.0780 -17.6561 97 | 0.0790 -19.4823 98 | 0.0800 -21.3222 99 | 0.0810 -23.0937 100 | 0.0820 -24.7637 101 | 0.0830 -26.2996 102 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx24.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 04:31:48 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/24 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb24.tpr -deffnm md-equilb24 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # GROtesk MACabre and Sinister 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -20.6162 19 | 0.0010 -20.4758 20 | 0.0020 -20.16 21 | 0.0030 -19.6644 22 | 0.0040 -19.0006 23 | 0.0050 -18.1954 24 | 0.0060 -17.2903 25 | 0.0070 -16.328 26 | 0.0080 -15.3623 27 | 0.0090 -14.4481 28 | 0.0100 -13.6232 29 | 0.0110 -12.9102 30 | 0.0120 -12.3118 31 | 0.0130 -11.8457 32 | 0.0140 -11.5203 33 | 0.0150 -11.343 34 | 0.0160 -11.3257 35 | 0.0170 -11.4731 36 | 0.0180 -11.7821 37 | 0.0190 -12.2429 38 | 0.0200 -12.8395 39 | 0.0210 -13.5522 40 | 0.0220 -14.3621 41 | 0.0230 -15.2294 42 | 0.0240 -16.1295 43 | 0.0250 -17.0282 44 | 0.0260 -17.8761 45 | 0.0270 -18.6254 46 | 0.0280 -19.2146 47 | 0.0290 -19.597 48 | 0.0300 -19.7477 49 | 0.0310 -19.6562 50 | 0.0320 -19.33 51 | 0.0330 -18.7954 52 | 0.0340 -18.0855 53 | 0.0350 -17.2349 54 | 0.0360 -16.2733 55 | 0.0370 -15.229 56 | 0.0380 -14.118 57 | 0.0390 -12.9761 58 | 0.0400 -11.8324 59 | 0.0410 -10.7302 60 | 0.0420 -9.73225 61 | 0.0430 -8.88068 62 | 0.0440 -8.22891 63 | 0.0450 -7.82932 64 | 0.0460 -7.71873 65 | 0.0470 -7.91301 66 | 0.0480 -8.41635 67 | 0.0490 -9.21427 68 | 0.0500 -10.2755 69 | 0.0510 -11.5569 70 | 0.0520 -13.0013 71 | 0.0530 -14.5285 72 | 0.0540 -16.079 73 | 0.0550 -17.5715 74 | 0.0560 -18.9551 75 | 0.0570 -20.1692 76 | 0.0580 -21.1798 77 | 0.0590 -21.9673 78 | 0.0600 -22.5171 79 | 0.0610 -22.8209 80 | 0.0620 -22.8773 81 | 0.0630 -22.6884 82 | 0.0640 -22.2673 83 | 0.0650 -21.6361 84 | 0.0660 -20.8411 85 | 0.0670 -19.9262 86 | 0.0680 -18.9526 87 | 0.0690 -17.9616 88 | 0.0700 -16.9973 89 | 0.0710 -16.0839 90 | 0.0720 -15.2341 91 | 0.0730 -14.4705 92 | 0.0740 -13.8231 93 | 0.0750 -13.3253 94 | 0.0760 -12.9988 95 | 0.0770 -12.855 96 | 0.0780 -12.8949 97 | 0.0790 -13.1125 98 | 0.0800 -13.4946 99 | 0.0810 -14.0235 100 | 0.0820 -14.6829 101 | 0.0830 -15.4523 102 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx25.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 05:02:09 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/25 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb25.tpr -deffnm md-equilb25 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gromacs Runs One Microsecond At Cannonball Speeds 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -10.9229 19 | 0.0010 -9.74414 20 | 0.0020 -8.61944 21 | 0.0030 -7.59938 22 | 0.0040 -6.71899 23 | 0.0050 -6.0274 24 | 0.0060 -5.5563 25 | 0.0070 -5.31802 26 | 0.0080 -5.31594 27 | 0.0090 -5.5419 28 | 0.0100 -5.97671 29 | 0.0110 -6.59269 30 | 0.0120 -7.36524 31 | 0.0130 -8.26474 32 | 0.0140 -9.25069 33 | 0.0150 -10.281 34 | 0.0160 -11.3234 35 | 0.0170 -12.3184 36 | 0.0180 -13.219 37 | 0.0190 -13.9874 38 | 0.0200 -14.6014 39 | 0.0210 -15.038 40 | 0.0220 -15.2843 41 | 0.0230 -15.3323 42 | 0.0240 -15.175 43 | 0.0250 -14.8105 44 | 0.0260 -14.2494 45 | 0.0270 -13.5183 46 | 0.0280 -12.6546 47 | 0.0290 -11.7092 48 | 0.0300 -10.7339 49 | 0.0310 -9.78111 50 | 0.0320 -8.8966 51 | 0.0330 -8.1224 52 | 0.0340 -7.4952 53 | 0.0350 -7.05634 54 | 0.0360 -6.82151 55 | 0.0370 -6.80767 56 | 0.0380 -7.02073 57 | 0.0390 -7.44735 58 | 0.0400 -8.06512 59 | 0.0410 -8.83148 60 | 0.0420 -9.70606 61 | 0.0430 -10.6462 62 | 0.0440 -11.6074 63 | 0.0450 -12.5507 64 | 0.0460 -13.4252 65 | 0.0470 -14.195 66 | 0.0480 -14.8259 67 | 0.0490 -15.2812 68 | 0.0500 -15.5353 69 | 0.0510 -15.5734 70 | 0.0520 -15.3976 71 | 0.0530 -15.0221 72 | 0.0540 -14.4723 73 | 0.0550 -13.7748 74 | 0.0560 -12.9551 75 | 0.0570 -12.044 76 | 0.0580 -11.07 77 | 0.0590 -10.08 78 | 0.0600 -9.10734 79 | 0.0610 -8.20076 80 | 0.0620 -7.40144 81 | 0.0630 -6.7373 82 | 0.0640 -6.22527 83 | 0.0650 -5.88848 84 | 0.0660 -5.73468 85 | 0.0670 -5.76666 86 | 0.0680 -5.98702 87 | 0.0690 -6.39096 88 | 0.0700 -6.9712 89 | 0.0710 -7.70404 90 | 0.0720 -8.56499 91 | 0.0730 -9.52265 92 | 0.0740 -10.5394 93 | 0.0750 -11.5888 94 | 0.0760 -12.6363 95 | 0.0770 -13.6504 96 | 0.0780 -14.5881 97 | 0.0790 -15.4079 98 | 0.0800 -16.069 99 | 0.0810 -16.5376 100 | 0.0820 -16.7941 101 | 0.0830 -16.8306 102 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx26.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 05:32:28 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/26 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb26.tpr -deffnm md-equilb26 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gyas ROwers Mature At Cryogenic Speed 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -21.6258 19 | 0.0010 -20.9841 20 | 0.0020 -19.9998 21 | 0.0030 -18.72 22 | 0.0040 -17.1969 23 | 0.0050 -15.4918 24 | 0.0060 -13.6703 25 | 0.0070 -11.8218 26 | 0.0080 -10.027 27 | 0.0090 -8.35305 28 | 0.0100 -6.8611 29 | 0.0110 -5.5882 30 | 0.0120 -4.5572 31 | 0.0130 -3.80591 32 | 0.0140 -3.34965 33 | 0.0150 -3.19675 34 | 0.0160 -3.3378 35 | 0.0170 -3.74225 36 | 0.0180 -4.35934 37 | 0.0190 -5.1245 38 | 0.0200 -5.97402 39 | 0.0210 -6.83097 40 | 0.0220 -7.63109 41 | 0.0230 -8.31765 42 | 0.0240 -8.83453 43 | 0.0250 -9.13001 44 | 0.0260 -9.17093 45 | 0.0270 -8.93015 46 | 0.0280 -8.40018 47 | 0.0290 -7.59066 48 | 0.0300 -6.53358 49 | 0.0310 -5.27958 50 | 0.0320 -3.89426 51 | 0.0330 -2.4509 52 | 0.0340 -1.03409 53 | 0.0350 0.274982 54 | 0.0360 1.40805 55 | 0.0370 2.27107 56 | 0.0380 2.8106 57 | 0.0390 2.98336 58 | 0.0400 2.76968 59 | 0.0410 2.16456 60 | 0.0420 1.18089 61 | 0.0430 -0.146674 62 | 0.0440 -1.77897 63 | 0.0450 -3.66227 64 | 0.0460 -5.75961 65 | 0.0470 -7.96936 66 | 0.0480 -10.236 67 | 0.0490 -12.4297 68 | 0.0500 -14.4872 69 | 0.0510 -16.2941 70 | 0.0520 -17.7923 71 | 0.0530 -18.8894 72 | 0.0540 -19.5355 73 | 0.0550 -19.6791 74 | 0.0560 -19.2945 75 | 0.0570 -18.3731 76 | 0.0580 -16.9293 77 | 0.0590 -15.0127 78 | 0.0600 -12.713 79 | 0.0610 -10.1046 80 | 0.0620 -7.30538 81 | 0.0630 -4.45953 82 | 0.0640 -1.70479 83 | 0.0650 0.859872 84 | 0.0660 3.15725 85 | 0.0670 5.08926 86 | 0.0680 6.57139 87 | 0.0690 7.56167 88 | 0.0700 7.98565 89 | 0.0710 7.83021 90 | 0.0720 7.09089 91 | 0.0730 5.79438 92 | 0.0740 3.99551 93 | 0.0750 1.74313 94 | 0.0760 -0.867457 95 | 0.0770 -3.73246 96 | 0.0780 -6.68521 97 | 0.0790 -9.57117 98 | 0.0800 -12.28 99 | 0.0810 -14.6694 100 | 0.0820 -16.6255 101 | 0.0830 -18.0694 102 | 0.0840 -18.9729 103 | 0.0850 -19.3275 104 | 0.0860 -19.1473 105 | 0.0870 -18.4674 106 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx27.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 06:02:47 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/27 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb27.tpr -deffnm md-equilb27 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -6.8584 19 | 0.0010 -6.30268 20 | 0.0020 -5.57489 21 | 0.0030 -4.68175 22 | 0.0040 -3.64518 23 | 0.0050 -2.50472 24 | 0.0060 -1.29808 25 | 0.0070 -0.0974058 26 | 0.0080 1.04637 27 | 0.0090 2.09348 28 | 0.0100 3.00007 29 | 0.0110 3.74169 30 | 0.0120 4.28821 31 | 0.0130 4.62525 32 | 0.0140 4.74549 33 | 0.0150 4.6512 34 | 0.0160 4.35751 35 | 0.0170 3.89203 36 | 0.0180 3.29463 37 | 0.0190 2.60967 38 | 0.0200 1.88157 39 | 0.0210 1.15412 40 | 0.0220 0.457841 41 | 0.0230 -0.181647 42 | 0.0240 -0.742244 43 | 0.0250 -1.19917 44 | 0.0260 -1.53731 45 | 0.0270 -1.74528 46 | 0.0280 -1.81629 47 | 0.0290 -1.75648 48 | 0.0300 -1.58044 49 | 0.0310 -1.30924 50 | 0.0320 -0.96911 51 | 0.0330 -0.584831 52 | 0.0340 -0.176441 53 | 0.0350 0.239138 54 | 0.0360 0.648703 55 | 0.0370 1.02884 56 | 0.0380 1.35733 57 | 0.0390 1.61598 58 | 0.0400 1.78102 59 | 0.0410 1.83851 60 | 0.0420 1.78525 61 | 0.0430 1.62965 62 | 0.0440 1.39166 63 | 0.0450 1.10053 64 | 0.0460 0.789724 65 | 0.0470 0.487285 66 | 0.0480 0.222876 67 | 0.0490 0.0263646 68 | 0.0500 -0.0787872 69 | 0.0510 -0.0697439 70 | 0.0520 0.068882 71 | 0.0530 0.344238 72 | 0.0540 0.749994 73 | 0.0550 1.26477 74 | 0.0560 1.84625 75 | 0.0570 2.44459 76 | 0.0580 3.01561 77 | 0.0590 3.5212 78 | 0.0600 3.9444 79 | 0.0610 4.26919 80 | 0.0620 4.4955 81 | 0.0630 4.62748 82 | 0.0640 4.66379 83 | 0.0650 4.59238 84 | 0.0660 4.39404 85 | 0.0670 4.05096 86 | 0.0680 3.55768 87 | 0.0690 2.91267 88 | 0.0700 2.146 89 | 0.0710 1.28939 90 | 0.0720 0.374596 91 | 0.0730 -0.556121 92 | 0.0740 -1.46573 93 | 0.0750 -2.32508 94 | 0.0760 -3.09313 95 | 0.0770 -3.73478 96 | 0.0780 -4.22198 97 | 0.0790 -4.5196 98 | 0.0800 -4.60665 99 | 0.0810 -4.4743 100 | 0.0820 -4.13149 101 | 0.0830 -3.59846 102 | 0.0840 -2.89885 103 | 0.0850 -2.06067 104 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx28.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 06:33:08 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/28 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb28.tpr -deffnm md-equilb28 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 1.92405 19 | 0.0010 2.29355 20 | 0.0020 2.70158 21 | 0.0030 3.13967 22 | 0.0040 3.58997 23 | 0.0050 4.02935 24 | 0.0060 4.4274 25 | 0.0070 4.76649 26 | 0.0080 5.03322 27 | 0.0090 5.22129 28 | 0.0100 5.33537 29 | 0.0110 5.38839 30 | 0.0120 5.39973 31 | 0.0130 5.38864 32 | 0.0140 5.36977 33 | 0.0150 5.35381 34 | 0.0160 5.35004 35 | 0.0170 5.36858 36 | 0.0180 5.42091 37 | 0.0190 5.51754 38 | 0.0200 5.66588 39 | 0.0210 5.86966 40 | 0.0220 6.12819 41 | 0.0230 6.43628 42 | 0.0240 6.78481 43 | 0.0250 7.15904 44 | 0.0260 7.54379 45 | 0.0270 7.92605 46 | 0.0280 8.29338 47 | 0.0290 8.62751 48 | 0.0300 8.90862 49 | 0.0310 9.11943 50 | 0.0320 9.24883 51 | 0.0330 9.29047 52 | 0.0340 9.24397 53 | 0.0350 9.11326 54 | 0.0360 8.90338 55 | 0.0370 8.621 56 | 0.0380 8.27427 57 | 0.0390 7.86942 58 | 0.0400 7.42232 59 | 0.0410 6.94482 60 | 0.0420 6.46 61 | 0.0430 5.98248 62 | 0.0440 5.53952 63 | 0.0450 5.14997 64 | 0.0460 4.82456 65 | 0.0470 4.56897 66 | 0.0480 4.38261 67 | 0.0490 4.26517 68 | 0.0500 4.21658 69 | 0.0510 4.23863 70 | 0.0520 4.33385 71 | 0.0530 4.50464 72 | 0.0540 4.75306 73 | 0.0550 5.07928 74 | 0.0560 5.47949 75 | 0.0570 5.94387 76 | 0.0580 6.46827 77 | 0.0590 7.03901 78 | 0.0600 7.64092 79 | 0.0610 8.26872 80 | 0.0620 8.91593 81 | 0.0630 9.5726 82 | 0.0640 10.2255 83 | 0.0650 10.8647 84 | 0.0660 11.4825 85 | 0.0670 12.0678 86 | 0.0680 12.5971 87 | 0.0690 13.0552 88 | 0.0700 13.4216 89 | 0.0710 13.681 90 | 0.0720 13.8205 91 | 0.0730 13.8336 92 | 0.0740 13.7214 93 | 0.0750 13.4908 94 | 0.0760 13.1515 95 | 0.0770 12.7219 96 | 0.0780 12.2128 97 | 0.0790 11.6437 98 | 0.0800 11.0287 99 | 0.0810 10.38 100 | 0.0820 9.70559 101 | 0.0830 9.02786 102 | 0.0840 8.35909 103 | 0.0850 7.71679 104 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx29.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 07:03:29 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/29 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb29.tpr -deffnm md-equilb29 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # GROningen MAchine for Chemical Simulation 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 14.1262 19 | 0.0010 13.6942 20 | 0.0020 13.1417 21 | 0.0030 12.4868 22 | 0.0040 11.7543 23 | 0.0050 10.9803 24 | 0.0060 10.2018 25 | 0.0070 9.46659 26 | 0.0080 8.81152 27 | 0.0090 8.2643 28 | 0.0100 7.85564 29 | 0.0110 7.59993 30 | 0.0120 7.51058 31 | 0.0130 7.59442 32 | 0.0140 7.85198 33 | 0.0150 8.27948 34 | 0.0160 8.86071 35 | 0.0170 9.58061 36 | 0.0180 10.3996 37 | 0.0190 11.2936 38 | 0.0200 12.2275 39 | 0.0210 13.1762 40 | 0.0220 14.1118 41 | 0.0230 15.0022 42 | 0.0240 15.8206 43 | 0.0250 16.5402 44 | 0.0260 17.147 45 | 0.0270 17.6229 46 | 0.0280 17.9663 47 | 0.0290 18.1834 48 | 0.0300 18.289 49 | 0.0310 18.3027 50 | 0.0320 18.2411 51 | 0.0330 18.1131 52 | 0.0340 17.9196 53 | 0.0350 17.661 54 | 0.0360 17.3403 55 | 0.0370 16.9729 56 | 0.0380 16.5702 57 | 0.0390 16.1612 58 | 0.0400 15.7763 59 | 0.0410 15.4414 60 | 0.0420 15.1734 61 | 0.0430 14.988 62 | 0.0440 14.8935 63 | 0.0450 14.8939 64 | 0.0460 14.9898 65 | 0.0470 15.178 66 | 0.0480 15.4479 67 | 0.0490 15.7827 68 | 0.0500 16.1627 69 | 0.0510 16.573 70 | 0.0520 16.9893 71 | 0.0530 17.3892 72 | 0.0540 17.7526 73 | 0.0550 18.0478 74 | 0.0560 18.2459 75 | 0.0570 18.31 76 | 0.0580 18.2112 77 | 0.0590 17.9299 78 | 0.0600 17.4607 79 | 0.0610 16.8193 80 | 0.0620 16.0327 81 | 0.0630 15.1426 82 | 0.0640 14.1997 83 | 0.0650 13.2445 84 | 0.0660 12.3149 85 | 0.0670 11.4305 86 | 0.0680 10.6112 87 | 0.0690 9.87798 88 | 0.0700 9.26528 89 | 0.0710 8.78679 90 | 0.0720 8.46727 91 | 0.0730 8.32636 92 | 0.0740 8.37614 93 | 0.0750 8.62028 94 | 0.0760 9.0478 95 | 0.0770 9.63982 96 | 0.0780 10.3666 97 | 0.0790 11.1941 98 | 0.0800 12.0867 99 | 0.0810 12.9949 100 | 0.0820 13.8864 101 | 0.0830 14.73 102 | 0.0840 15.4986 103 | 0.0850 16.1781 104 | 0.0860 16.7532 105 | 0.0870 17.2052 106 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx3.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 17:54:09 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/3 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb3.tpr -deffnm md-equilb3 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # GROup of MAchos and Cynical Suckers 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -171.754 19 | 0.0010 -171.956 20 | 0.0020 -172.167 21 | 0.0030 -172.388 22 | 0.0040 -172.617 23 | 0.0050 -172.844 24 | 0.0060 -173.068 25 | 0.0070 -173.28 26 | 0.0080 -173.475 27 | 0.0090 -173.645 28 | 0.0100 -173.789 29 | 0.0110 -173.911 30 | 0.0120 -174.012 31 | 0.0130 -174.098 32 | 0.0140 -174.17 33 | 0.0150 -174.233 34 | 0.0160 -174.288 35 | 0.0170 -174.336 36 | 0.0180 -174.376 37 | 0.0190 -174.405 38 | 0.0200 -174.421 39 | 0.0210 -174.424 40 | 0.0220 -174.418 41 | 0.0230 -174.411 42 | 0.0240 -174.407 43 | 0.0250 -174.412 44 | 0.0260 -174.427 45 | 0.0270 -174.448 46 | 0.0280 -174.473 47 | 0.0290 -174.491 48 | 0.0300 -174.496 49 | 0.0310 -174.48 50 | 0.0320 -174.44 51 | 0.0330 -174.376 52 | 0.0340 -174.289 53 | 0.0350 -174.179 54 | 0.0360 -174.047 55 | 0.0370 -173.893 56 | 0.0380 -173.718 57 | 0.0390 -173.519 58 | 0.0400 -173.292 59 | 0.0410 -173.039 60 | 0.0420 -172.761 61 | 0.0430 -172.453 62 | 0.0440 -172.121 63 | 0.0450 -171.769 64 | 0.0460 -171.402 65 | 0.0470 -171.028 66 | 0.0480 -170.648 67 | 0.0490 -170.271 68 | 0.0500 -169.895 69 | 0.0510 -169.516 70 | 0.0520 -169.129 71 | 0.0530 -168.732 72 | 0.0540 -168.327 73 | 0.0550 -167.917 74 | 0.0560 -167.514 75 | 0.0570 -167.126 76 | 0.0580 -166.757 77 | 0.0590 -166.41 78 | 0.0600 -166.087 79 | 0.0610 -165.777 80 | 0.0620 -165.472 81 | 0.0630 -165.163 82 | 0.0640 -164.849 83 | 0.0650 -164.537 84 | 0.0660 -164.237 85 | 0.0670 -163.954 86 | 0.0680 -163.699 87 | 0.0690 -163.476 88 | 0.0700 -163.282 89 | 0.0710 -163.113 90 | 0.0720 -162.961 91 | 0.0730 -162.818 92 | 0.0740 -162.675 93 | 0.0750 -162.53 94 | 0.0760 -162.386 95 | 0.0770 -162.25 96 | 0.0780 -162.129 97 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx30.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sun Nov 29 07:33:43 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/30 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb30.tpr -deffnm md-equilb30 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gyas ROwers Mature At Cryogenic Speed 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 16.7608 19 | 0.0010 16.4366 20 | 0.0020 16.2106 21 | 0.0030 16.0921 22 | 0.0040 16.0799 23 | 0.0050 16.1726 24 | 0.0060 16.3639 25 | 0.0070 16.6418 26 | 0.0080 16.9954 27 | 0.0090 17.4086 28 | 0.0100 17.864 29 | 0.0110 18.3474 30 | 0.0120 18.843 31 | 0.0130 19.3348 32 | 0.0140 19.8078 33 | 0.0150 20.2466 34 | 0.0160 20.6336 35 | 0.0170 20.963 36 | 0.0180 21.2264 37 | 0.0190 21.4192 38 | 0.0200 21.5459 39 | 0.0210 21.6054 40 | 0.0220 21.6027 41 | 0.0230 21.5408 42 | 0.0240 21.4234 43 | 0.0250 21.2555 44 | 0.0260 21.0442 45 | 0.0270 20.7979 46 | 0.0280 20.5298 47 | 0.0290 20.2448 48 | 0.0300 19.9509 49 | 0.0310 19.657 50 | 0.0320 19.3736 51 | 0.0330 19.1092 52 | 0.0340 18.8738 53 | 0.0350 18.6713 54 | 0.0360 18.5017 55 | 0.0370 18.3543 56 | 0.0380 18.2156 57 | 0.0390 18.0692 58 | 0.0400 17.9 59 | 0.0410 17.7014 60 | 0.0420 17.4688 61 | 0.0430 17.2061 62 | 0.0440 16.919 63 | 0.0450 16.612 64 | 0.0460 16.292 65 | 0.0470 15.9653 66 | 0.0480 15.6433 67 | 0.0490 15.3384 68 | 0.0500 15.0705 69 | 0.0510 14.8584 70 | 0.0520 14.7253 71 | 0.0530 14.6838 72 | 0.0540 14.7429 73 | 0.0550 14.9069 74 | 0.0560 15.1776 75 | 0.0570 15.5552 76 | 0.0580 16.0389 77 | 0.0590 16.6301 78 | 0.0600 17.3319 79 | 0.0610 18.1392 80 | 0.0620 19.0401 81 | 0.0630 20.0289 82 | 0.0640 21.0699 83 | 0.0650 22.1232 84 | 0.0660 23.1611 85 | 0.0670 24.1393 86 | 0.0680 25.0354 87 | 0.0690 25.8242 88 | 0.0700 26.4781 89 | 0.0710 26.9831 90 | 0.0720 27.3283 91 | 0.0730 27.5082 92 | 0.0740 27.5229 93 | 0.0750 27.3784 94 | 0.0760 27.0872 95 | 0.0770 26.6711 96 | 0.0780 26.1578 97 | 0.0790 25.5784 98 | 0.0800 24.9534 99 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx4.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 18:24:29 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/4 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb4.tpr -deffnm md-equilb4 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Glycine aRginine prOline Methionine Alanine Cystine Serine 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -161.864 19 | 0.0010 -162.166 20 | 0.0020 -162.53 21 | 0.0030 -162.941 22 | 0.0040 -163.381 23 | 0.0050 -163.831 24 | 0.0060 -164.275 25 | 0.0070 -164.7 26 | 0.0080 -165.088 27 | 0.0090 -165.435 28 | 0.0100 -165.731 29 | 0.0110 -165.975 30 | 0.0120 -166.174 31 | 0.0130 -166.337 32 | 0.0140 -166.474 33 | 0.0150 -166.597 34 | 0.0160 -166.714 35 | 0.0170 -166.831 36 | 0.0180 -166.949 37 | 0.0190 -167.066 38 | 0.0200 -167.174 39 | 0.0210 -167.27 40 | 0.0220 -167.353 41 | 0.0230 -167.428 42 | 0.0240 -167.509 43 | 0.0250 -167.607 44 | 0.0260 -167.733 45 | 0.0270 -167.89 46 | 0.0280 -168.077 47 | 0.0290 -168.282 48 | 0.0300 -168.488 49 | 0.0310 -168.678 50 | 0.0320 -168.832 51 | 0.0330 -168.943 52 | 0.0340 -169.011 53 | 0.0350 -169.042 54 | 0.0360 -169.046 55 | 0.0370 -169.033 56 | 0.0380 -169.011 57 | 0.0390 -168.982 58 | 0.0400 -168.948 59 | 0.0410 -168.903 60 | 0.0420 -168.837 61 | 0.0430 -168.742 62 | 0.0440 -168.61 63 | 0.0450 -168.442 64 | 0.0460 -168.25 65 | 0.0470 -168.046 66 | 0.0480 -167.85 67 | 0.0490 -167.671 68 | 0.0500 -167.516 69 | 0.0510 -167.383 70 | 0.0520 -167.259 71 | 0.0530 -167.129 72 | 0.0540 -166.975 73 | 0.0550 -166.783 74 | 0.0560 -166.556 75 | 0.0570 -166.301 76 | 0.0580 -166.028 77 | 0.0590 -165.751 78 | 0.0600 -165.473 79 | 0.0610 -165.198 80 | 0.0620 -164.923 81 | 0.0630 -164.64 82 | 0.0640 -164.326 83 | 0.0650 -163.963 84 | 0.0660 -163.538 85 | 0.0670 -163.05 86 | 0.0680 -162.507 87 | 0.0690 -161.931 88 | 0.0700 -161.349 89 | 0.0710 -160.781 90 | 0.0720 -160.25 91 | 0.0730 -159.764 92 | 0.0740 -159.321 93 | 0.0750 -158.905 94 | 0.0760 -158.499 95 | 0.0770 -158.095 96 | 0.0780 -157.707 97 | 0.0790 -157.36 98 | 0.0800 -157.077 99 | 0.0810 -156.873 100 | 0.0820 -156.749 101 | 0.0830 -156.691 102 | 0.0840 -156.674 103 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx5.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 18:54:59 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/5 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb5.tpr -deffnm md-equilb5 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Good ROcking Metal Altar for Chronical Sinners 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -151.492 19 | 0.0010 -151.785 20 | 0.0020 -152.141 21 | 0.0030 -152.548 22 | 0.0040 -152.994 23 | 0.0050 -153.469 24 | 0.0060 -153.954 25 | 0.0070 -154.44 26 | 0.0080 -154.91 27 | 0.0090 -155.352 28 | 0.0100 -155.754 29 | 0.0110 -156.105 30 | 0.0120 -156.409 31 | 0.0130 -156.67 32 | 0.0140 -156.888 33 | 0.0150 -157.071 34 | 0.0160 -157.22 35 | 0.0170 -157.333 36 | 0.0180 -157.411 37 | 0.0190 -157.45 38 | 0.0200 -157.448 39 | 0.0210 -157.401 40 | 0.0220 -157.311 41 | 0.0230 -157.181 42 | 0.0240 -157.02 43 | 0.0250 -156.832 44 | 0.0260 -156.622 45 | 0.0270 -156.391 46 | 0.0280 -156.142 47 | 0.0290 -155.878 48 | 0.0300 -155.603 49 | 0.0310 -155.322 50 | 0.0320 -155.039 51 | 0.0330 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0.0810 -161.61 100 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx6.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 19:25:20 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/6 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb6.tpr -deffnm md-equilb6 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Gromacs Runs One Microsecond At Cannonball Speeds 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -148.863 19 | 0.0010 -149.308 20 | 0.0020 -149.872 21 | 0.0030 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-157.373 70 | 0.0520 -157.157 71 | 0.0530 -156.937 72 | 0.0540 -156.724 73 | 0.0550 -156.532 74 | 0.0560 -156.363 75 | 0.0570 -156.218 76 | 0.0580 -156.091 77 | 0.0590 -155.972 78 | 0.0600 -155.84 79 | 0.0610 -155.677 80 | 0.0620 -155.464 81 | 0.0630 -155.188 82 | 0.0640 -154.847 83 | 0.0650 -154.451 84 | 0.0660 -154.014 85 | 0.0670 -153.545 86 | 0.0680 -153.044 87 | 0.0690 -152.521 88 | 0.0700 -151.985 89 | 0.0710 -151.43 90 | 0.0720 -150.851 91 | 0.0730 -150.248 92 | 0.0740 -149.637 93 | 0.0750 -149.047 94 | 0.0760 -148.523 95 | 0.0770 -148.099 96 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx7.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 19:55:42 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/7 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb7.tpr -deffnm md-equilb7 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # God Rules Over Mankind, Animals, Cosmos and Such 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -143.753 19 | 0.0010 -143.423 20 | 0.0020 -143.132 21 | 0.0030 -142.932 22 | 0.0040 -142.858 23 | 0.0050 -142.926 24 | 0.0060 -143.13 25 | 0.0070 -143.441 26 | 0.0080 -143.816 27 | 0.0090 -144.195 28 | 0.0100 -144.517 29 | 0.0110 -144.737 30 | 0.0120 -144.851 31 | 0.0130 -144.886 32 | 0.0140 -144.877 33 | 0.0150 -144.853 34 | 0.0160 -144.829 35 | 0.0170 -144.813 36 | 0.0180 -144.803 37 | 0.0190 -144.785 38 | 0.0200 -144.733 39 | 0.0210 -144.615 40 | 0.0220 -144.413 41 | 0.0230 -144.143 42 | 0.0240 -143.85 43 | 0.0250 -143.582 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-142.08 92 | 0.0740 -142.063 93 | 0.0750 -142 94 | 0.0760 -141.869 95 | 0.0770 -141.682 96 | 0.0780 -141.489 97 | 0.0790 -141.354 98 | 0.0800 -141.34 99 | 0.0810 -141.488 100 | 0.0820 -141.814 101 | 0.0830 -142.305 102 | -------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx8.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 20:26:07 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/8 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb8.tpr -deffnm md-equilb8 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # GROningen Mixture of Alchemy and Childrens' 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-------------------------------------------------------------------------------- /stilbene_vacuum/profile-100fs/pullx9.xvg: -------------------------------------------------------------------------------- 1 | # This file was created Sat Nov 28 20:56:26 2020 2 | # Created by: 3 | # :-) GROMACS - mdrun_mpi_d, 2022-dev-UNCHECKED (double precision) (-: 4 | # 5 | # Executable: /fs3/d118/d118/shared/GRM-CP2K/exe/mdrun_mpi_d 6 | # Data prefix: /work/d118/d118/hjudge/Bioexcel/QMMM/interface/gromacs-CP2KInterface/install 7 | # Working dir: /fs3/d118/d118/dmorozov/stilbene_vacuum/us_frames/9 8 | # Command line: 9 | # mdrun_mpi_d -npme 0 -s md-equilb9.tpr -deffnm md-equilb9 10 | # mdrun_mpi_d is part of G R O M A C S: 11 | # 12 | # Great Red Owns Many ACres of Sand 13 | # 14 | @ title "Pull COM" 15 | @ xaxis label "Time (ps)" 16 | @ yaxis label "Position (nm, deg)" 17 | @TYPE xy 18 | 0.0000 -127.05 19 | 0.0010 -127.115 20 | 0.0020 -127.215 21 | 0.0030 -127.355 22 | 0.0040 -127.535 23 | 0.0050 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stilbene16.tpr 9 | stilbene17.tpr 10 | stilbene18.tpr 11 | stilbene19.tpr 12 | stilbene2.tpr 13 | stilbene20.tpr 14 | stilbene21.tpr 15 | stilbene22.tpr 16 | stilbene23.tpr 17 | stilbene24.tpr 18 | stilbene25.tpr 19 | stilbene26.tpr 20 | stilbene27.tpr 21 | stilbene28.tpr 22 | stilbene29.tpr 23 | stilbene3.tpr 24 | stilbene30.tpr 25 | stilbene4.tpr 26 | stilbene5.tpr 27 | stilbene6.tpr 28 | stilbene7.tpr 29 | stilbene8.tpr 30 | stilbene9.tpr 31 | -------------------------------------------------------------------------------- /stilbene_vacuum/qmmm_md_umbrella.mdp: -------------------------------------------------------------------------------- 1 | ; Run parameters 2 | integrator = md 3 | dt = 0.001 4 | tinit = 0 5 | nsteps = 10000 ; 10 ps 6 | nstcomm = 1 7 | ; Output parameters 8 | nstxout = 1000 ; every 1 ps 9 | nstvout = 1000 10 | nstfout = 1000 11 | nstlog = 1 12 | nstxtcout = 1 ; every 1 fs 13 | nstenergy = 1 14 | nstcalcenergy = 1 15 | 16 | energygrps = System ; Which energy group(s) to write to disk 17 | 18 | rlist = 1.0 ; Short-range neighborlist cut-off distance [nm] 19 | rcoulomb = 1.0 ; Long range coulomb cut-off distance [nm] 20 | rvdw = 1.0 ; Long range vdw cut-off distance [nm] 21 | 22 | cutoff-scheme = Verlet 23 | nstlist = 1 ; Freq, to update neighbour list 24 | pbc = xyz ; With periodic boundary conditions 25 | 26 | tcoupl = v-rescale ;Temperature coupling options 27 | nsttcouple = 1 28 | tc-grps = System 29 | tau-t = 0.5 30 | ref-t = 300 31 | 32 | 33 | ; GENERATE VELOCITIES FOR STARTUP RUN 34 | gen-vel = yes 35 | gen-temp = 300 36 | gen-seed = -1 37 | 38 | ; Pull code 39 | pull = yes 40 | pull_ncoords = 1 ; only one reaction coordinate 41 | pull_ngroups = 4 ; four groups defining one reaction coordinate 42 | pull_group1_name = group1 43 | pull_group2_name = group2 44 | pull_group3_name = group3 45 | pull_group4_name = group4 46 | pull_coord1_type = umbrella ; harmonic potential 47 | pull_coord1_geometry = dihedral 48 | pull_coord1_dim = Y Y Y 49 | pull_coord1_groups = 1 2 2 3 3 4 50 | pull-coord1-init = @umbr@ 51 | pull_coord1_rate = 0.00 ; restrain in place 52 | pull_coord1_k = 418.4 ; kJ mol^-1 nm^-2 53 | pull-nstxout = 1 54 | pull-nstfout = 1 55 | 56 | ; CP2K QMMM parameters 57 | 58 | qmmm-cp2k-active = true 59 | qmmm-cp2k-qmgroup = QMatoms 60 | qmmm-cp2k-qmmethod = PBE 61 | qmmm-cp2k-qmcharge = 0 62 | qmmm-cp2k-qmmultiplicity = 1 63 | -------------------------------------------------------------------------------- /stilbene_vacuum/run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J stilbene_vacuum 3 | #SBATCH --time=00:20:00 4 | #SBATCH --partition=test 5 | 6 | #SBATCH --nodes=1 7 | #SBATCH --tasks-per-node=32 8 | #SBATCH --cpus-per-task=4 9 | 10 | export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK 11 | export OMP_PLACES=cores 12 | 13 | srun gmx mdrun -npme 0 -s stilbene.tpr --------------------------------------------------------------------------------