├── CCU-Tutorial ├── Input-Files │ ├── Choline_itp │ │ ├── choline_DES.itp │ │ └── choline_atomtypes_DES.itp │ ├── Cl_itp │ │ ├── cl_DES.itp │ │ └── cl_atomtypes_DES.itp │ ├── Urea_itp │ │ ├── urea_DES.itp │ │ └── urea_atomtypes_DES.itp │ ├── choline_cl_urea.cpt │ ├── choline_cl_urea.gro │ ├── choline_cl_urea.top │ └── grompp_prod.mdp ├── Output-Files │ ├── choline_cl_urea_prod.cpt │ ├── choline_cl_urea_prod.edr │ ├── choline_cl_urea_prod.gro │ ├── choline_cl_urea_prod.log │ ├── choline_cl_urea_prod.tpr │ └── density.log └── Tutorial-README.txt ├── DES ├── ITP │ ├── 2,2,2-trifluoroacetamide_DES.itp │ ├── 2,2,2-trifluoroacetamide_atomtypes_DES.itp │ ├── N,N-diethylethanolammonium_DES.itp │ ├── N,N-diethylethanolammonium_atomtypes_DES.itp │ ├── N-ethyl-N,N-dimethylethanolammonium_DES.itp │ ├── N-ethyl-N,N-dimethylethanolammonium_atomtypes_DES.itp │ ├── acetamide_DES.itp │ ├── acetamide_atomtypes_DES.itp │ ├── choline_DES.itp │ ├── choline_atomtypes_DES.itp │ ├── cl_DES.itp │ ├── cl_atomtypes_DES.itp │ ├── ethgly_DES.itp │ ├── ethgly_atomtypes_DES.itp │ ├── ethylammonium_DES.itp │ ├── ethylammonium_atomtypes_DES.itp │ ├── glycerol_DES.itp │ ├── glycerol_atomtypes_DES.itp │ ├── levulinic_DES.itp │ ├── levulinic_atomtypes_DES.itp │ ├── malonic_DES.itp │ ├── malonic_atomtypes_DES.itp │ ├── oxalic_DES.itp │ ├── oxalic_atomtypes_DES.itp │ ├── phenol_DES.itp │ ├── phenol_atomtypes_DES.itp │ ├── urea_DES.itp │ └── urea_atomtypes_DES.itp ├── PDBs │ ├── 2,2,2-trifluoroacetamide.pdb │ ├── N,N-diethylethanolammonium.pdb │ ├── N-ethyl-N,N-dimethylethanolammonium.pdb │ ├── acetamide.pdb │ ├── chloride.pdb │ ├── choline.pdb │ ├── ethylammonium.pdb │ ├── ethylene_glycol.pdb │ ├── glycerol.pdb │ ├── levulinic.pdb │ ├── malonic.pdb │ ├── oxalic_acid.pdb │ ├── phenol.pdb │ └── urea.pdb └── TOP │ ├── CCEtg_DES.top │ ├── CCGly_DES.top │ ├── CCLev_DES.top │ ├── CCMal_DES.top │ ├── CCOx_DES.top │ ├── CCPhe_2.1_DES.top │ ├── CCPhe_3.1_DES.top │ ├── CCU_DES.top │ └── template.top ├── LICENSE └── README.md /CCU-Tutorial/Input-Files/Choline_itp/choline_DES.itp: -------------------------------------------------------------------------------- 1 | ; Choline cation [Chol] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | CHOL 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 CS 1 CHOL CS 1 -0.131 12.011 21 | 2 HS 1 CHOL HS 1 0.068 1.008 22 | 3 HS 1 CHOL HS 1 0.068 1.008 23 | 4 NA 1 CHOL NA 1 0.791 14.007 24 | 5 CW 1 CHOL CW 1 0.132 12.011 25 | 6 HW 1 CHOL HW 1 0.034 1.008 26 | 7 HW 1 CHOL HW 1 0.034 1.008 27 | 8 OY 1 CHOL OY 1 -0.468 15.999 28 | 9 HY 1 CHOL HY 1 0.275 1.008 29 | 10 CA 1 CHOL CA 1 -0.100 12.011 30 | 11 HA 1 CHOL HA 1 0.033 1.008 31 | 12 HA 1 CHOL HA 1 0.033 1.008 32 | 13 HA 1 CHOL HA 1 0.033 1.008 33 | 14 CA 1 CHOL CA 1 -0.100 12.011 34 | 15 HA 1 CHOL HA 1 0.033 1.008 35 | 16 HA 1 CHOL HA 1 0.033 1.008 36 | 17 HA 1 CHOL HA 1 0.033 1.008 37 | 18 CA 1 CHOL CA 1 -0.100 12.011 38 | 19 HA 1 CHOL HA 1 0.033 1.008 39 | 20 HA 1 CHOL HA 1 0.033 1.008 40 | 21 HA 1 CHOL HA 1 0.033 1.008 41 | 42 | [ bonds ] 43 | ; ai aj funct c0(nm) c1(kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 44 | 11 10 1 0.1099 284512.000 ; 1.0990 340 HA-CA 45 | 12 10 1 0.1099 284512.000 ; 1.0990 340 HA-CA 46 | 13 10 1 0.1099 284512.000 ; 1.0990 340 HA-CA 47 | 15 14 1 0.1099 284512.000 ; 1.0990 340 HA-CA 48 | 16 14 1 0.1099 284512.000 ; 1.0990 340 HA-CA 49 | 17 14 1 0.1099 284512.000 ; 1.0990 340 HA-CA 50 | 19 18 1 0.1099 284512.000 ; 1.0990 340 HA-CA 51 | 20 18 1 0.1099 284512.000 ; 1.0990 340 HA-CA 52 | 21 18 1 0.1099 284512.000 ; 1.0990 340 HA-CA 53 | 10 4 1 0.1498 410032.000 ; 1.4980 490 CA-NA 54 | 14 4 1 0.1498 410032.000 ; 1.4980 490 CA-NA 55 | 18 4 1 0.1498 410032.000 ; 1.4980 490 CA-NA 56 | 4 1 1 0.1516 410032.000 ; 1.5160 490 NA-CS 57 | 1 2 1 0.10805 284512.000 ; 1.0805 340 CS-HS 58 | 1 3 1 0.10805 284512.000 ; 1.0805 340 CS-HS 59 | 1 5 1 0.1521 265265.600 ; 1.5210 317 CS-CW 60 | 5 6 1 0.1085 284512.000 ; 1.0850 340 CW-HW 61 | 5 7 1 0.1085 284512.000 ; 1.0850 340 CW-HW 62 | 5 8 1 0.1395 376560.000 ; 1.3950 450 CW-OY 63 | 8 9 1 0.0949 462750.400 ; 0.9490 553 OY-HY 64 | 65 | [ angles ] 66 | ; ai aj ak funct c0(deg) c1(kj mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 67 | 11 10 12 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 68 | 11 10 13 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 69 | 12 10 13 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 70 | 15 14 16 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 71 | 15 14 17 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 72 | 16 14 17 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 73 | 19 18 20 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 74 | 19 18 21 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 75 | 20 18 21 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 76 | 11 10 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 77 | 12 10 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 78 | 13 10 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 79 | 15 14 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 80 | 16 14 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 81 | 17 14 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 82 | 19 18 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 83 | 20 18 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 84 | 21 18 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 85 | 10 4 1 1 110.20 433.4624 ; 110.20 51.8 CA-NA-CS 86 | 14 4 1 1 110.20 433.4624 ; 110.20 51.8 CA-NA-CS 87 | 18 4 1 1 110.20 433.4624 ; 110.20 51.8 CA-NA-CS 88 | 4 1 2 1 106.40 292.8800 ; 106.40 35.0 NA-CS-HS 89 | 4 1 3 1 106.40 292.8800 ; 106.40 35.0 NA-CS-HS 90 | 4 1 5 1 116.60 585.7600 ; 116.60 70.0 NA-CS-CW 91 | 1 5 6 1 108.30 292.8800 ; 108.30 35.0 CS-CW-HW 92 | 1 5 7 1 108.30 292.8800 ; 108.30 35.0 CS-CW-HW 93 | 1 5 8 1 109.60 669.4400 ; 109.60 80.0 CS-CW-OY 94 | 2 1 5 1 109.30 292.8800 ; 109.30 35.0 HS-CS-CW 95 | 3 1 5 1 109.30 292.8800 ; 109.30 35.0 HS-CS-CW 96 | 6 5 8 1 111.60 292.8800 ; 111.60 35.0 HW-CW-OY 97 | 7 5 8 1 111.60 292.8800 ; 111.60 35.0 HW-CW-OY 98 | 5 8 9 1 110.90 292.8800 ; 110.90 35.0 CW-OY-HY 99 | 10 4 14 1 108.73 460.2400 ; 108.73 55.0 CA-NA-CA 100 | 10 4 18 1 108.73 460.2400 ; 108.73 55.0 CA-NA-CA 101 | 14 4 18 1 108.73 460.2400 ; 108.73 55.0 CA-NA-CA 102 | 2 1 3 1 108.60 292.8800 ; 108.60 35.0 HS-CS-HS 103 | 6 5 7 1 107.40 292.8800 ; 107.40 35.0 HW-CW-Hw 104 | 105 | [ dihedrals ] 106 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 107 | 5 1 4 10 5 0.4184 2.30120 2.71960 0.0000 ; 0.100 0.550 0.650 0.000 CW-CS-NA-CA 108 | 5 1 4 14 5 0.4184 2.30120 2.71960 0.0000 ; 0.100 0.550 0.650 0.000 CW-CS-NA-CA 109 | 5 1 4 18 5 0.4184 2.30120 2.71960 0.0000 ; 0.100 0.550 0.650 0.000 CW-CS-NA-CA 110 | 10 4 14 15 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 111 | 10 4 14 16 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 112 | 10 4 14 17 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 113 | 10 4 18 19 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 114 | 10 4 18 20 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 115 | 10 4 18 21 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 116 | 14 4 10 11 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 117 | 14 4 10 12 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 118 | 14 4 10 13 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 119 | 14 4 18 19 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 120 | 14 4 18 20 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 121 | 14 4 18 21 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 122 | 18 4 10 11 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 123 | 18 4 10 12 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 124 | 18 4 10 13 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 125 | 18 4 14 15 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 126 | 18 4 14 16 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 127 | 18 4 14 17 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 128 | 1 4 10 11 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 129 | 1 4 10 12 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 130 | 1 4 10 13 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 131 | 1 4 14 15 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 132 | 1 4 14 16 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 133 | 1 4 14 17 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 134 | 1 4 18 19 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 135 | 1 4 18 20 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 136 | 1 4 18 21 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 137 | 2 1 4 10 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 138 | 2 1 4 14 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 139 | 2 1 4 18 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 140 | 3 1 4 10 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 141 | 3 1 4 14 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 142 | 3 1 4 18 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 143 | 8 5 1 4 5 -25.1040 -20.92000 13.38880 0.0000 ; -6.000 -5.000 3.200 0.000 OY-CW-CS-NA 144 | 8 5 1 2 5 -2.0920 -10.46000 1.04600 0.0000 ; -0.500 -2.500 0.250 0.000 OY-CW-CS-HS 145 | 8 5 1 3 5 -2.0920 -10.46000 1.04600 0.0000 ; -0.500 -2.500 0.250 0.000 OY-CW-CS-HS 146 | 6 5 1 4 5 -25.1040 -29.28800 3.13800 0.0000 ; -6.000 -7.000 0.750 0.000 HW-CW-CS-NA 147 | 7 5 1 4 5 -25.1040 -29.28800 3.13800 0.0000 ; -6.000 -7.000 0.750 0.000 HW-CW-CS-NA 148 | 6 5 1 2 5 25.1040 -12.55200 8.36800 0.0000 ; 6.000 -3.000 2.000 0.000 HW-CW-CS-HS 149 | 6 5 1 3 5 25.1040 -12.55200 8.36800 0.0000 ; 6.000 -3.000 2.000 0.000 HW-CW-CS-HS 150 | 7 5 1 2 5 25.1040 -12.55200 8.36800 0.0000 ; 6.000 -3.000 2.000 0.000 HW-CW-CS-HS 151 | 7 5 1 3 5 25.1040 -12.55200 8.36800 0.0000 ; 6.000 -3.000 2.000 0.000 HW-CW-CS-HS 152 | 9 8 5 1 5 -1.4895 -0.72802 1.46440 0.0000 ; -0.356 -0.174 0.350 0.000 HY-OY-CW-CS 153 | 9 8 5 6 5 -12.552 4.18400 -8.36800 0.0000 ; -3.000 1.000 -2.000 0.000 HY-OY-CW-HW 154 | 9 8 5 7 5 -12.552 4.18400 -8.36800 0.0000 ; -3.000 1.000 -2.000 0.000 HY-OY-CW-HW 155 | 10 4 14 18 5 0.000 8.36800 0.00000 0.0000 ; 0.000 2.000 0.000 0.000 CA-NA-CA-CA improper 156 | 1 4 10 14 5 0.000 8.36800 0.00000 0.0000 ; 0.000 2.000 0.000 0.000 CS-NA-CA-CA improper 157 | 1 4 10 18 5 0.000 8.36800 0.00000 0.0000 ; 0.000 2.000 0.000 0.000 CS-NA-CA-CA improper 158 | 1 4 14 18 5 0.000 8.36800 0.00000 0.0000 ; 0.000 2.000 0.000 0.000 CS-NA-CA-CA improper 159 | 160 | -------------------------------------------------------------------------------- /CCU-Tutorial/Input-Files/Choline_itp/choline_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Choline cation [Chol] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma (Ang.) epsilon (kcal/mol) 16 | CS 12.011 -0.131 A 0.3500 0.276144 ; 3.50 0.066 17 | HS 1.008 0.068 A 0.2600 0.125520 ; 2.60 0.030 18 | NA 14.007 0.791 A 0.3250 0.711280 ; 3.25 0.170 19 | CA 12.011 -0.100 A 0.3500 0.276144 ; 3.50 0.066 20 | CW 12.011 0.132 A 0.3500 0.276144 ; 3.50 0.066 21 | OY 15.999 -0.468 A 0.3070 0.711280 ; 3.07 0.170 22 | HA 1.008 0.033 A 0.2500 0.125520 ; 2.50 0.030 23 | HW 1.008 0.034 A 0.2200 0.125520 ; 2.20 0.030 24 | HY 1.008 0.275 A 0.0000 0.000000 ; 0.00 0.000 25 | 26 | -------------------------------------------------------------------------------- /CCU-Tutorial/Input-Files/Cl_itp/cl_DES.itp: -------------------------------------------------------------------------------- 1 | ; Chlorine anion [cl] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | Cl 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 Cl 1 Cl Cl 1 -0.800 35.45 21 | 22 | -------------------------------------------------------------------------------- /CCU-Tutorial/Input-Files/Cl_itp/cl_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Chlorine anion [cl] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma (Ang.) epsilon (kcal/mol) 16 | Cl 35.45 -0.800 A 0.377 0.619232 ; 3.77 0.1480 17 | -------------------------------------------------------------------------------- /CCU-Tutorial/Input-Files/Urea_itp/urea_DES.itp: -------------------------------------------------------------------------------- 1 | ; Urea HBD [UREA] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | UREA 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 C 1 UREA C 1 0.124 12.011 21 | 2 O 1 UREA O 1 -0.322 15.999 22 | 3 N 1 UREA N 1 -0.453 14.007 23 | 4 N 1 UREA N 1 -0.453 14.007 24 | 5 HT 1 UREA HT 1 0.276 1.008 25 | 6 HC 1 UREA HC 1 0.276 1.008 26 | 7 HT 1 UREA HT 1 0.276 1.008 27 | 8 HC 1 UREA HC 1 0.276 1.008 28 | 29 | [ bonds ] 30 | ; ai aj funct c0 (nm) c1 (kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 31 | 1 2 1 0.1229 476976.000 ; 1.229 570 C-O 32 | 1 3 1 0.1335 410032.000 ; 1.335 490 C-N 33 | 1 4 1 0.1335 410032.000 ; 1.335 490 C-N 34 | 3 7 1 0.1010 363171.200 ; 1.010 434 N-HT 35 | 3 8 1 0.1010 363171.200 ; 1.010 434 N-HC 36 | 4 5 1 0.1010 363171.200 ; 1.010 434 N-HT 37 | 4 6 1 0.1010 363171.200 ; 1.010 434 N-HC 38 | 39 | [ angles ] 40 | ; ai aj ak funct c0 (deg) c1 (kJ mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 41 | 2 1 3 1 122.9 669.440 ; 122.9 80 O-C-N 42 | 2 1 4 1 122.9 669.440 ; 122.9 80 O-C-N 43 | 1 3 7 1 119.8 292.880 ; 119.8 35 C-N-HT 44 | 1 3 8 1 119.8 292.880 ; 119.8 35 C-N-HC 45 | 1 4 5 1 119.8 292.880 ; 119.8 35 C-N-HT 46 | 1 4 6 1 119.8 292.880 ; 119.8 35 C-N-HC 47 | 3 1 4 1 114.2 585.760 ; 114.2 70 N-C-N 48 | 5 4 6 1 120.0 292.880 ; 120.0 35 HT-N-HC 49 | 7 3 8 1 120.0 292.880 ; 120.0 35 HT-N-HC 50 | 51 | [ dihedrals ] 52 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 53 | 2 1 3 7 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 O-C-N-HT 54 | 2 1 3 8 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 O-C-N-HC 55 | 2 1 4 5 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 O-C-N-HT 56 | 2 1 4 6 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 O-C-N-HC 57 | 7 3 1 4 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 HT-N-C-N 58 | 8 3 1 4 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 HC-N-C-N 59 | 5 4 1 3 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 HT-N-C-N 60 | 6 4 1 3 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 HC-N-C-N 61 | 7 3 1 8 5 0.0000 20.9200 0.0000 0.0000 ; 0.00 5.00 0.00 0.00 HT-N-C-HC improper 62 | 5 4 1 6 5 0.0000 20.9200 0.0000 0.0000 ; 0.00 5.00 0.00 0.00 HT-N-C-HC improper 63 | 2 1 3 4 5 0.0000 87.8640 0.0000 0.0000 ; 0.00 21.00 0.00 0.00 O-C-N-N improper 64 | 65 | -------------------------------------------------------------------------------- /CCU-Tutorial/Input-Files/Urea_itp/urea_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Urea HBD [UREA] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma(Ang.) epsilon(kcal/mol) 16 | C 12.011 0.124 A 0.375 0.65898 ; 3.75 0.1575 17 | O 15.999 -0.322 A 0.296 1.31796 ; 2.96 0.3150 18 | N 14.007 -0.453 A 0.355 1.06692 ; 3.55 0.2550 19 | HT 1.008 0.276 A 0.000 0.00000 ; 0.00 0.0000 20 | HC 1.008 0.276 A 0.000 0.00000 ; 0.00 0.0000 21 | -------------------------------------------------------------------------------- /CCU-Tutorial/Input-Files/choline_cl_urea.cpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orlandoacevedo/DES/15a82205a1531ff081a831f9ccb3914dc003fef1/CCU-Tutorial/Input-Files/choline_cl_urea.cpt -------------------------------------------------------------------------------- /CCU-Tutorial/Input-Files/choline_cl_urea.top: -------------------------------------------------------------------------------- 1 | #define _FF_OPLS 2 | #define _FF_OPLSAA 3 | 4 | [defaults] 5 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 6 | 1 3 yes 0.5 0.5 7 | 8 | ;;;LOAD ATOM TYPES 9 | #include "Choline_itp/choline_atomtypes_DES.itp" 10 | #include "Cl_itp/cl_atomtypes_DES.itp" 11 | #include "Urea_itp/urea_atomtypes_DES.itp" 12 | 13 | ;;;LOAD MOLECULES *.itp 14 | #include "Choline_itp/choline_DES.itp" 15 | #include "Cl_itp/cl_DES.itp" 16 | #include "Urea_itp/urea_DES.itp" 17 | 18 | [system] 19 | ; Name 20 | Neat CHOL Cl UREA 21 | 22 | [molecules] 23 | CHOL 500 24 | Cl 500 25 | UREA 1000 26 | -------------------------------------------------------------------------------- /CCU-Tutorial/Input-Files/grompp_prod.mdp: -------------------------------------------------------------------------------- 1 | ; RUN CONTROL PARAMETERS = 2 | 3 | integrator = md ; md integrator 4 | tinit = 10000 ; [ps] starting time for run 5 | dt = 0.001 ; [ps] time step for integration 6 | nsteps = 50000000 ; maximum number of steps to integrate, 0.001 * 50,000,000 = 50000 ps = 50 ns 7 | comm-mode = Linear ; Remove center of mass translation 8 | 9 | ; OUTPUT CONTROL OPTIONS = 10 | nstxout = 25000 ; [steps] freq to write coordinates to trajectory 11 | nstvout = 25000 ; [steps] freq to write velocities to trajectory 12 | nstfout = 25000 ; [steps] freq to write forces to trajectory 13 | nstlog = 2000 ; [steps] freq to write energies to log file 14 | nstenergy = 10000 ; group(s) to write to energy file 15 | nstxout-compressed = 10000 ; freq to write coordinates to xtc trajectory 16 | 17 | 18 | ; NEIGHBORSEARCHING PARAMETERS = 19 | cutoff-scheme = verlet ; This option has an explicit, exact cut-off at rvdw=rcoulomb. 20 | nstlist = 20 ; [steps] freq to update neighbor list 21 | ns_type = grid ; method of updating neighbor list 22 | pbc = xyz ; periodic boundary conditions in all directions 23 | rlist = 1.6 ; [nm] cut-off distance for the short-range neighbor list 24 | verlet-buffer-tolerance = 0.005 ; sets the maximum allowed error for pair interactions per particle. Indirectly sets rlist 25 | 26 | ; OPTIONS FOR ELECTROSTATICS AND VDW = 27 | coulombtype = PME ; Particle-Mesh Ewald electrostatics 28 | rcoulomb = 1.6 ; [nm] distance for Coulomb cut-off 29 | vdw_type = PME ; twin-range cut-off with rlist where rvdw >= rlist 30 | rvdw = 1.6 ; [nm] distance for LJ cut-off 31 | fourierspacing = 0.15 ; [nm] grid spacing for FFT grid when using PME 32 | pme_order = 4 ; interpolation order for PME, 4 = cubic 33 | ewald_rtol = 1e-05 ; relative strength of Ewald-shifted potential at rcoulomb 34 | 35 | ; OPTIONS FOR WEAK COUPLING ALGORITHMS = 36 | tcoupl = v-rescale ; temperature coupling method 37 | tc-grps = System ; groups to couple seperately to temperature bath 38 | tau_t = 1.0 ; [ps] time constant for coupling 39 | ref_t = 298.15 ; reference temperature for coupling 40 | Pcoupl = Berendsen ; pressure coupling method 41 | Pcoupltype = isotropic ; pressure coupling in x-y-z directions 42 | tau_p = 1.0 ; [ps] time constant for coupling 43 | compressibility = 4.5e-5 ; [bar^-1] compressibility 44 | ref_p = 1.0 ; bar ; reference pressure for coupling 45 | 46 | ; GENERATE VELOCITIES FOR STARTUP RUN = 47 | gen_vel = no ; velocity generation turned on/off 48 | 49 | ; OPTIONS FOR BONDS = 50 | constraints = hbonds 51 | constraint_algorithm = lincs 52 | unconstrained_start = no 53 | lincs_order = 4 54 | lincs_warnangle = 30 55 | morse = no 56 | lincs_iter = 2 57 | 58 | -------------------------------------------------------------------------------- /CCU-Tutorial/Output-Files/choline_cl_urea_prod.cpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orlandoacevedo/DES/15a82205a1531ff081a831f9ccb3914dc003fef1/CCU-Tutorial/Output-Files/choline_cl_urea_prod.cpt -------------------------------------------------------------------------------- /CCU-Tutorial/Output-Files/choline_cl_urea_prod.edr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orlandoacevedo/DES/15a82205a1531ff081a831f9ccb3914dc003fef1/CCU-Tutorial/Output-Files/choline_cl_urea_prod.edr -------------------------------------------------------------------------------- /CCU-Tutorial/Output-Files/choline_cl_urea_prod.tpr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/orlandoacevedo/DES/15a82205a1531ff081a831f9ccb3914dc003fef1/CCU-Tutorial/Output-Files/choline_cl_urea_prod.tpr -------------------------------------------------------------------------------- /CCU-Tutorial/Output-Files/density.log: -------------------------------------------------------------------------------- 1 | 2 | Statistics over 50000001 steps [ 10000.0000 through 60000.0000 ps ], 1 data sets 3 | All statistics are over 500001 points 4 | 5 | Energy Average Err.Est. RMSD Tot-Drift 6 | ------------------------------------------------------------------------------- 7 | Density 1148.05 0.36 1.47814 1.61561 (kg/m^3) 8 | -------------------------------------------------------------------------------- /CCU-Tutorial/Tutorial-README.txt: -------------------------------------------------------------------------------- 1 | GROMACS Tutorial For Simulating Deep Eutectic Solvents 2 | 3 | ***************************************************************************************************************************** 4 | I. Introduction 5 | 6 | In this tutorial, the reader will learn how to run a molecular dynamics simulation on the CCU Deep Eutectic Solvent system using the GROMACS software package. Provided with this tutorial are GROMACS input files, a pre-equilibrated box of CCU that was constructed using the packmol software (http://www.ime.unicamp.br/~martinez/packmol/home.shtml), and output files to compare results. All simulations in this tutorial were run using GROMACS 5.0.7, which is highly recommended. 7 | 8 | ***************************************************************************************************************************** 9 | II. Setting up parameters in GROMACS 10 | 11 | Since the parameters implemented in the simulation are not available in the force fields built into GROMACS, .itp files are necessary. The .itp files contain the nonbonded and bonded parameters for the cation choline, anion Cl, and hydrogen bond donor urea. It is also important to note the units for each parameter, as it is necessary to convert the traditional OPLS-AA units to GROMACS. The conversions are listed as followed. 12 | 13 | Non-Bonded: 14 | 1) Lennard-jones values are converted from Å to nm and kcal/mol to kJ/mol. 15 | 16 | Bonded: 17 | 1) Equilibrium bond distances are converted from Å to nm. 18 | 2) Bond force constants are converted from kcal/mol Å^2 to kJ/mol nm^2. For this case multiply the force constants by 4.184*2*100. 19 | 3) Angle force constants are converted from kcal/mol rad^2 to kJ/mol rad^2. For this case multiply the force constants by 4.184*2. 20 | 4) Fourier coefficients are converted from kcal/mol to kJ/mol. 21 | 22 | These conversions have already been made in the .itp files included with this tutorial and in the github repository. In order to call the .itp files for the simulation, GROMACS uses .top files. As you will see in the .top file, each of the .itp files are being sourced for choline, chloride, and urea. Additionally, the .top file is where combination rules and fudge factors are stated, as well as the name of the system and how many of each individual molecule there are in the box. 23 | 24 | With the molecular parameters set up, the run parameters need to be selected for the simulations. This is done through the use of .mdp files. Using the .mdp file provided, a production run using a NPT ensemble will be executed for 50ns. If different run inputs are desired, the reader is referenced to the GROMACS user manual (ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf). 25 | ***************************************************************************************************************************** 26 | III. Running A GROMACS Simulation 27 | 28 | The main integration engine of GROMACS is a tool called ‘mdrun’, which requires a pre-processed run input file with the extension .tpr. This file contains the system’s coordinates, topology, and run parameters. Therefore the following files are needed: 29 | 30 | .gro - coordinate file for the system of interest 31 | .top - topology file that contains molecule/ion parameters 32 | .cpt - checkpoint file from a previous molecular dynamics run 33 | .mdp - file that contains the run parameters for the simulation 34 | 35 | To create the .tpr file use the command: 36 | 37 | grompp –f grompp_prod.mdp –c input.gro –p input.top -t input.cpt –o output.tpr 38 | 39 | Make sure there are no errors in the output. If everything is correct the .tpr can now be used. 40 | 41 | To submit the molecular dynamics job, use the following command: 42 | 43 | mdrun –deffnm output.tpr –v 44 | 45 | the flag –deffnm will set default names for all of the output files and –v will include more output information in the .log file. As the simulation is running you can track it by looking into the .log file to see how many steps have been performed. Once the simulation is finished the following output files should be available: 46 | 47 | - Output.edr 48 | - Output.cpt 49 | - Output.xtc 50 | - Output.trr 51 | - Output.log 52 | 53 | ***************************************************************************************************************************** 54 | IV. Post Trajectory Analysis 55 | 56 | There are many properties that can be calculated once a production run is completed in GROMACS. In this tutorial the density will be determined for the CCU system. 57 | 58 | ####### 59 | Density 60 | ####### 61 | 62 | To determine the density of the system, the ‘g_energy’ tool can be used. To use g_energy type the following command: 63 | 64 | g_energy –f output.edr > density.log 65 | 66 | A menu will pop up where density can then be selected for GROMACS to analyze. In the density.log file, the average density, error estimation, RMSD, and total drift of the trajectory will be provided. 67 | 68 | -------------------------------------------------------------------------------- /DES/ITP/2,2,2-trifluoroacetamide_DES.itp: -------------------------------------------------------------------------------- 1 | ; 2,2,2-trifluoroacetamide 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ moleculetype ] 18 | ; name nrexcl 19 | HBD 3 20 | 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass 24 | 1 opls_800 1 HBD N00 1 25 | 2 opls_801 1 HBD C01 1 26 | 3 opls_802 1 HBD O02 1 27 | 4 opls_803 1 HBD C03 1 28 | 5 opls_805 1 HBD F04 1 29 | 6 opls_805 1 HBD F05 1 30 | 7 opls_805 1 HBD F06 1 31 | 8 opls_807 1 HBD H07 1 32 | 9 opls_807 1 HBD H08 1 33 | 34 | 35 | [ bonds ] 36 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 37 | 2 1 1 0.1335 410032.000 38 | 3 2 1 0.1229 476976.000 39 | 4 2 1 0.1522 265265.600 40 | 5 4 1 0.1360 307105.600 41 | 6 4 1 0.1360 307105.600 42 | 7 4 1 0.1360 307105.600 43 | 8 1 1 0.1010 363171.200 44 | 9 1 1 0.1010 363171.200 45 | 46 | 47 | [ angles ] 48 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 49 | 1 2 3 1 122.900 669.440 50 | 1 2 4 1 116.600 585.760 51 | 2 4 5 1 109.500 418.400 52 | 2 4 6 1 109.500 418.400 53 | 2 4 7 1 109.500 418.400 54 | 2 1 8 1 119.800 292.880 55 | 2 1 9 1 119.800 292.880 56 | 5 4 6 1 109.100 644.336 57 | 3 2 4 1 120.400 669.440 58 | 5 4 7 1 109.100 644.336 59 | 8 1 9 1 120.000 292.880 60 | 6 4 7 1 109.100 644.336 61 | 62 | 63 | [ dihedrals ] 64 | ; IMPROPER DIHEDRAL ANGLES 65 | ; ai aj ak al func deg k(kj mol-1) mp 66 | 4 2 1 3 4 180.000 43.932 2 67 | 9 1 2 8 4 180.000 10.460 2 68 | 69 | 70 | [ dihedrals ] 71 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 72 | 5 4 2 1 3 12.219 6.123 -5.113 -13.23 0.000 0.000 73 | 6 4 2 1 3 12.219 6.123 -5.113 -13.23 0.000 0.000 74 | 7 4 2 1 3 12.219 6.123 -5.113 -13.23 0.000 0.000 75 | 7 4 2 3 3 0.000 0.000 0.000 0.000 0.000 0.000 76 | 5 4 2 3 3 0.000 0.000 0.000 0.000 0.000 0.000 77 | 6 4 2 3 3 0.000 0.000 0.000 0.000 0.000 0.000 78 | 9 1 2 4 3 20.502 0.000 -20.502 0.000 0.000 0.000 79 | 8 1 2 4 3 20.502 0.000 -20.502 0.000 0.000 0.000 80 | 8 1 2 3 3 20.502 0.000 -20.502 0.000 0.000 0.000 81 | 9 1 2 3 3 20.502 0.000 -20.502 0.000 0.000 0.000 82 | 83 | 84 | -------------------------------------------------------------------------------- /DES/ITP/2,2,2-trifluoroacetamide_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; 2,2,2-trifluoroacetamide 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ atomtypes ] 18 | ; type mass charge ptype sigma(nm) epsilon(kj/mol) 19 | opls_800 14.007 -0.686 A 3.25000E-01 7.11280E-01 20 | opls_801 12.011 0.606 A 3.55000E-01 2.92880E-01 21 | opls_802 15.999 -0.502 A 2.96000E-01 8.78640E-01 22 | opls_803 12.011 0.082 A 3.50000E-01 2.76144E-01 23 | opls_805 18.998 -0.108 A 2.90000E-01 2.51040E-01 24 | opls_807 1.008 0.412 A 0.00000E+00 0.00000E+00 25 | 26 | 27 | -------------------------------------------------------------------------------- /DES/ITP/N,N-diethylethanolammonium_DES.itp: -------------------------------------------------------------------------------- 1 | ; N,N-diethylethanolammonium 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ moleculetype ] 18 | ; name nrexcl 19 | MOL 3 20 | 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass 24 | 1 CT 1 MOL C00 1 25 | 2 CA 1 MOL C01 1 26 | 3 N 1 MOL N02 1 27 | 4 HN 1 MOL H03 1 28 | 5 CA 1 MOL C04 1 29 | 6 CT 1 MOL C05 1 30 | 7 CS 1 MOL C06 1 31 | 8 CK 1 MOL C07 1 32 | 9 OH 1 MOL O08 1 33 | 10 HT 1 MOL H09 1 34 | 11 HT 1 MOL H0A 1 35 | 12 HT 1 MOL H0B 1 36 | 13 HA 1 MOL H0C 1 37 | 14 HA 1 MOL H0D 1 38 | 15 HA 1 MOL H0E 1 39 | 16 HA 1 MOL H0F 1 40 | 17 HT 1 MOL H0G 1 41 | 18 HT 1 MOL H0H 1 42 | 19 HT 1 MOL H0I 1 43 | 20 HS 1 MOL H0J 1 44 | 21 HS 1 MOL H0K 1 45 | 22 HK 1 MOL H0M 1 46 | 23 HK 1 MOL H0N 1 47 | 24 HO 1 MOL H0O 1 48 | 49 | 50 | [ bonds ] 51 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 52 | 2 1 1 0.1529 224262.400 53 | 3 2 1 0.1471 307105.600 54 | 4 3 1 0.1010 363171.200 55 | 5 3 1 0.1471 307105.600 56 | 6 5 1 0.1529 224262.400 57 | 7 3 1 0.1471 307105.600 58 | 8 7 1 0.1529 224262.400 59 | 9 8 1 0.1410 267776.000 60 | 10 1 1 0.1090 284512.000 61 | 11 1 1 0.1090 284512.000 62 | 12 1 1 0.1090 284512.000 63 | 13 2 1 0.1090 284512.000 64 | 14 2 1 0.1090 284512.000 65 | 15 5 1 0.1090 284512.000 66 | 16 5 1 0.1090 284512.000 67 | 17 6 1 0.1090 284512.000 68 | 18 6 1 0.1090 284512.000 69 | 19 6 1 0.1090 284512.000 70 | 20 7 1 0.1090 284512.000 71 | 21 7 1 0.1090 284512.000 72 | 22 8 1 0.1090 284512.000 73 | 23 8 1 0.1090 284512.000 74 | 24 9 1 0.0945 462750.400 75 | 76 | 77 | [ angles ] 78 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 79 | 1 2 3 1 111.200 669.440 80 | 2 3 4 1 107.640 269.031 81 | 2 3 5 1 113.000 418.400 82 | 3 5 6 1 111.200 669.440 83 | 2 3 7 1 113.000 418.400 84 | 3 7 8 1 111.200 669.440 85 | 7 8 9 1 109.500 418.400 86 | 2 1 10 1 110.700 313.800 87 | 2 1 11 1 110.700 313.800 88 | 2 1 12 1 110.700 313.800 89 | 1 2 13 1 110.700 313.800 90 | 1 2 14 1 110.700 313.800 91 | 3 5 15 1 109.500 292.880 92 | 3 5 16 1 109.500 292.880 93 | 5 6 17 1 110.700 313.800 94 | 5 6 18 1 110.700 313.800 95 | 5 6 19 1 110.700 313.800 96 | 3 7 20 1 109.500 292.880 97 | 3 7 21 1 109.500 292.880 98 | 7 8 22 1 110.700 313.800 99 | 7 8 23 1 110.700 313.800 100 | 8 9 24 1 108.500 460.240 101 | 15 5 16 1 107.800 276.144 102 | 17 6 19 1 107.800 276.144 103 | 3 2 14 1 109.500 292.880 104 | 6 5 16 1 110.700 313.800 105 | 17 6 18 1 107.800 276.144 106 | 18 6 19 1 107.800 276.144 107 | 4 3 7 1 107.640 269.031 108 | 9 8 23 1 109.500 292.880 109 | 5 3 7 1 113.000 418.400 110 | 22 8 23 1 107.800 276.144 111 | 4 3 5 1 107.640 269.031 112 | 20 7 21 1 107.800 276.144 113 | 11 1 12 1 107.800 276.144 114 | 13 2 14 1 107.800 276.144 115 | 9 8 22 1 109.500 292.880 116 | 10 1 12 1 107.800 276.144 117 | 10 1 11 1 107.800 276.144 118 | 3 2 13 1 109.500 292.880 119 | 8 7 21 1 110.700 313.800 120 | 6 5 15 1 110.700 313.800 121 | 8 7 20 1 110.700 313.800 122 | 123 | 124 | [ dihedrals ] 125 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 126 | 6 5 3 2 3 3.042 -1.351 0.519 -2.209 0.000 0.000 127 | 8 7 3 5 3 3.042 -1.351 0.519 -2.209 0.000 0.000 128 | 8 7 3 2 3 3.042 -1.351 0.519 -2.209 0.000 0.000 129 | 8 7 3 4 3 0.726 2.178 0.000 -2.904 0.000 0.000 130 | 6 5 3 4 3 0.726 2.178 0.000 -2.904 0.000 0.000 131 | 7 3 5 6 3 3.042 -1.351 0.519 -2.209 0.000 0.000 132 | 5 3 2 1 3 3.042 -1.351 0.519 -2.209 0.000 0.000 133 | 7 3 2 1 3 3.042 -1.351 0.519 -2.209 0.000 0.000 134 | 4 3 2 1 3 0.726 2.178 0.000 -2.904 0.000 0.000 135 | 17 6 5 16 3 0.628 1.883 0.000 -2.510 0.000 0.000 136 | 23 8 7 21 3 0.628 1.883 0.000 -2.510 0.000 0.000 137 | 14 2 1 10 3 0.628 1.883 0.000 -2.510 0.000 0.000 138 | 18 6 5 15 3 0.628 1.883 0.000 -2.510 0.000 0.000 139 | 13 2 1 11 3 0.628 1.883 0.000 -2.510 0.000 0.000 140 | 13 2 1 10 3 0.628 1.883 0.000 -2.510 0.000 0.000 141 | 13 2 1 12 3 0.628 1.883 0.000 -2.510 0.000 0.000 142 | 19 6 5 15 3 0.628 1.883 0.000 -2.510 0.000 0.000 143 | 18 6 5 16 3 0.628 1.883 0.000 -2.510 0.000 0.000 144 | 22 8 7 20 3 0.628 1.883 0.000 -2.510 0.000 0.000 145 | 19 6 5 16 3 0.628 1.883 0.000 -2.510 0.000 0.000 146 | 17 6 5 15 3 0.628 1.883 0.000 -2.510 0.000 0.000 147 | 22 8 7 21 3 0.628 1.883 0.000 -2.510 0.000 0.000 148 | 23 8 7 20 3 0.628 1.883 0.000 -2.510 0.000 0.000 149 | 14 2 1 11 3 0.628 1.883 0.000 -2.510 0.000 0.000 150 | 14 2 1 12 3 0.628 1.883 0.000 -2.510 0.000 0.000 151 | 10 1 2 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 152 | 19 6 5 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 153 | 11 1 2 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 154 | 22 8 7 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 155 | 23 8 7 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 156 | 17 6 5 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 157 | 18 6 5 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 158 | 12 1 2 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 159 | 20 7 8 9 3 0.979 2.937 0.000 -3.916 0.000 0.000 160 | 21 7 8 9 3 0.979 2.937 0.000 -3.916 0.000 0.000 161 | 14 2 3 7 3 0.632 1.895 0.000 -2.527 0.000 0.000 162 | 15 5 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 163 | 21 7 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 164 | 21 7 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 165 | 13 2 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 166 | 14 2 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 167 | 13 2 3 7 3 0.632 1.895 0.000 -2.527 0.000 0.000 168 | 16 5 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 169 | 15 5 3 7 3 0.632 1.895 0.000 -2.527 0.000 0.000 170 | 16 5 3 7 3 0.632 1.895 0.000 -2.527 0.000 0.000 171 | 20 7 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 172 | 20 7 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 173 | 20 7 3 4 3 0.546 1.638 0.000 -2.184 0.000 0.000 174 | 13 2 3 4 3 0.546 1.638 0.000 -2.184 0.000 0.000 175 | 16 5 3 4 3 0.546 1.638 0.000 -2.184 0.000 0.000 176 | 14 2 3 4 3 0.546 1.638 0.000 -2.184 0.000 0.000 177 | 15 5 3 4 3 0.546 1.638 0.000 -2.184 0.000 0.000 178 | 21 7 3 4 3 0.546 1.638 0.000 -2.184 0.000 0.000 179 | 24 9 8 7 3 -0.444 3.833 0.728 -4.117 0.000 0.000 180 | 24 9 8 22 3 0.736 2.209 0.000 -2.946 0.000 0.000 181 | 24 9 8 23 3 0.736 2.209 0.000 -2.946 0.000 0.000 182 | 9 8 7 3 3 16.736 -16.736 0.000 0.000 0.000 0.000 183 | 184 | 185 | -------------------------------------------------------------------------------- /DES/ITP/N,N-diethylethanolammonium_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; N,N-diethylethanolammonium 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ atomtypes ] 18 | ; type mass charge ptype sigma(nm) epsilon(kj/mol) 19 | CT 12.011 -0.17 A 3.50000E-01 2.76144E-01 20 | HT 1.008 0.36 A 2.50000E-01 1.25520E-01 21 | CA 12.011 -0.36 A 3.50000E-01 2.76144E-01 22 | HA 1.008 0.136 A 2.50000E-01 1.25520E-01 23 | CS 12.011 -0.41 A 3.50000E-01 2.76144E-01 24 | HS 1.008 0.102 A 2.50000E-01 1.25520E-01 25 | CK 12.011 -0.45 A 3.50000E-01 2.76144E-01 26 | HK 1.008 0.173 A 2.50000E-01 1.25520E-01 27 | OH 15.999 -0.448 A 3.12000E-01 7.11280E-01 28 | HO 1.008 0.163 A 0.00000E+00 0.00000E+00 29 | N 14.007 -0.129 A 3.25000E-01 7.11280E-01 30 | HN 1.008 0.08 A 0.00000E+00 0.00000E+00 31 | 32 | 33 | -------------------------------------------------------------------------------- /DES/ITP/N-ethyl-N,N-dimethylethanolammonium_DES.itp: -------------------------------------------------------------------------------- 1 | ; N-ethyl-N,N-dimethylethanolammonium 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ moleculetype ] 18 | ; name nrexcl 19 | MOL 3 20 | 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass 24 | 1 CT 1 MOL C00 1 25 | 2 CA 1 MOL C01 1 26 | 3 N 1 MOL N02 1 27 | 4 CG 1 MOL C03 1 28 | 5 CG 1 MOL C04 1 29 | 6 CS 1 MOL C05 1 30 | 7 CK 1 MOL C06 1 31 | 8 OH 1 MOL O07 1 32 | 9 HT 1 MOL H08 1 33 | 10 HT 1 MOL H09 1 34 | 11 HT 1 MOL H0A 1 35 | 12 HA 1 MOL H0B 1 36 | 13 HA 1 MOL H0C 1 37 | 14 HG 1 MOL H0D 1 38 | 15 HG 1 MOL H0E 1 39 | 16 HG 1 MOL H0F 1 40 | 17 HG 1 MOL H0G 1 41 | 18 HG 1 MOL H0H 1 42 | 19 HG 1 MOL H0I 1 43 | 20 HS 1 MOL H0J 1 44 | 21 HS 1 MOL H0K 1 45 | 22 HK 1 MOL H0M 1 46 | 23 HK 1 MOL H0N 1 47 | 24 HO 1 MOL H0O 1 48 | 49 | 50 | [ bonds ] 51 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 52 | 2 1 1 0.1529 224262.400 53 | 3 2 1 0.1471 307105.600 54 | 4 3 1 0.1471 307105.600 55 | 5 3 1 0.1471 307105.600 56 | 6 3 1 0.1471 307105.600 57 | 7 6 1 0.1529 224262.400 58 | 8 7 1 0.1410 267776.000 59 | 9 1 1 0.1090 284512.000 60 | 10 1 1 0.1090 284512.000 61 | 11 1 1 0.1090 284512.000 62 | 12 2 1 0.1090 284512.000 63 | 13 2 1 0.1090 284512.000 64 | 14 4 1 0.1090 284512.000 65 | 15 4 1 0.1090 284512.000 66 | 16 4 1 0.1090 284512.000 67 | 17 5 1 0.1090 284512.000 68 | 18 5 1 0.1090 284512.000 69 | 19 5 1 0.1090 284512.000 70 | 20 6 1 0.1090 284512.000 71 | 21 6 1 0.1090 284512.000 72 | 22 7 1 0.1090 284512.000 73 | 23 7 1 0.1090 284512.000 74 | 24 8 1 0.0945 462750.400 75 | 76 | 77 | [ angles ] 78 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 79 | 1 2 3 1 111.200 669.440 80 | 2 3 4 1 113.000 418.400 81 | 2 3 5 1 113.000 418.400 82 | 2 3 6 1 113.000 418.400 83 | 3 6 7 1 111.200 669.440 84 | 6 7 8 1 109.500 418.400 85 | 2 1 9 1 110.700 313.800 86 | 2 1 10 1 110.700 313.800 87 | 2 1 11 1 110.700 313.800 88 | 1 2 12 1 110.700 313.800 89 | 1 2 13 1 110.700 313.800 90 | 3 4 14 1 109.500 292.880 91 | 3 4 15 1 109.500 292.880 92 | 3 4 16 1 109.500 292.880 93 | 3 5 17 1 109.500 292.880 94 | 3 5 18 1 109.500 292.880 95 | 3 5 19 1 109.500 292.880 96 | 3 6 20 1 109.500 292.880 97 | 3 6 21 1 109.500 292.880 98 | 6 7 22 1 110.700 313.800 99 | 6 7 23 1 110.700 313.800 100 | 7 8 24 1 108.500 460.240 101 | 17 5 18 1 107.800 276.144 102 | 15 4 16 1 107.800 276.144 103 | 12 2 13 1 107.800 276.144 104 | 22 7 23 1 107.800 276.144 105 | 14 4 16 1 107.800 276.144 106 | 18 5 19 1 107.800 276.144 107 | 4 3 5 1 113.000 418.400 108 | 8 7 23 1 109.500 292.880 109 | 7 6 21 1 110.700 313.800 110 | 14 4 15 1 107.800 276.144 111 | 3 2 12 1 109.500 292.880 112 | 8 7 22 1 109.500 292.880 113 | 10 1 11 1 107.800 276.144 114 | 3 2 13 1 109.500 292.880 115 | 9 1 10 1 107.800 276.144 116 | 17 5 19 1 107.800 276.144 117 | 9 1 11 1 107.800 276.144 118 | 4 3 6 1 113.000 418.400 119 | 5 3 6 1 113.000 418.400 120 | 20 6 21 1 107.800 276.144 121 | 7 6 20 1 110.700 313.800 122 | 123 | 124 | [ dihedrals ] 125 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 126 | 7 6 3 5 3 3.042 -1.351 0.519 -2.209 0.000 0.000 127 | 7 6 3 4 3 3.042 -1.351 0.519 -2.209 0.000 0.000 128 | 7 6 3 2 3 3.042 -1.351 0.519 -2.209 0.000 0.000 129 | 4 3 2 1 3 3.042 -1.351 0.519 -2.209 0.000 0.000 130 | 6 3 2 1 3 3.042 -1.351 0.519 -2.209 0.000 0.000 131 | 5 3 2 1 3 3.042 -1.351 0.519 -2.209 0.000 0.000 132 | 13 2 1 10 3 0.628 1.883 0.000 -2.510 0.000 0.000 133 | 12 2 1 11 3 0.628 1.883 0.000 -2.510 0.000 0.000 134 | 23 7 6 20 3 0.628 1.883 0.000 -2.510 0.000 0.000 135 | 13 2 1 11 3 0.628 1.883 0.000 -2.510 0.000 0.000 136 | 12 2 1 10 3 0.628 1.883 0.000 -2.510 0.000 0.000 137 | 13 2 1 9 3 0.628 1.883 0.000 -2.510 0.000 0.000 138 | 22 7 6 20 3 0.628 1.883 0.000 -2.510 0.000 0.000 139 | 22 7 6 21 3 0.628 1.883 0.000 -2.510 0.000 0.000 140 | 23 7 6 21 3 0.628 1.883 0.000 -2.510 0.000 0.000 141 | 12 2 1 9 3 0.628 1.883 0.000 -2.510 0.000 0.000 142 | 23 7 6 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 143 | 22 7 6 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 144 | 9 1 2 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 145 | 10 1 2 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 146 | 11 1 2 3 3 0.803 2.410 0.000 -3.213 0.000 0.000 147 | 20 6 7 8 3 0.979 2.937 0.000 -3.916 0.000 0.000 148 | 21 6 7 8 3 0.979 2.937 0.000 -3.916 0.000 0.000 149 | 13 2 3 6 3 0.632 1.895 0.000 -2.527 0.000 0.000 150 | 13 2 3 4 3 0.632 1.895 0.000 -2.527 0.000 0.000 151 | 18 5 3 4 3 0.632 1.895 0.000 -2.527 0.000 0.000 152 | 14 4 3 6 3 0.632 1.895 0.000 -2.527 0.000 0.000 153 | 20 6 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 154 | 20 6 3 4 3 0.632 1.895 0.000 -2.527 0.000 0.000 155 | 14 4 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 156 | 21 6 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 157 | 15 4 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 158 | 21 6 3 4 3 0.632 1.895 0.000 -2.527 0.000 0.000 159 | 16 4 3 6 3 0.632 1.895 0.000 -2.527 0.000 0.000 160 | 18 5 3 6 3 0.632 1.895 0.000 -2.527 0.000 0.000 161 | 20 6 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 162 | 15 4 3 6 3 0.632 1.895 0.000 -2.527 0.000 0.000 163 | 16 4 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 164 | 13 2 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 165 | 12 2 3 5 3 0.632 1.895 0.000 -2.527 0.000 0.000 166 | 16 4 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 167 | 17 5 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 168 | 18 5 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 169 | 17 5 3 6 3 0.632 1.895 0.000 -2.527 0.000 0.000 170 | 15 4 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 171 | 19 5 3 4 3 0.632 1.895 0.000 -2.527 0.000 0.000 172 | 14 4 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 173 | 19 5 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 174 | 17 5 3 4 3 0.632 1.895 0.000 -2.527 0.000 0.000 175 | 19 5 3 6 3 0.632 1.895 0.000 -2.527 0.000 0.000 176 | 12 2 3 4 3 0.632 1.895 0.000 -2.527 0.000 0.000 177 | 12 2 3 6 3 0.632 1.895 0.000 -2.527 0.000 0.000 178 | 21 6 3 2 3 0.632 1.895 0.000 -2.527 0.000 0.000 179 | 24 8 7 6 3 -0.444 3.833 0.728 -4.117 0.000 0.000 180 | 24 8 7 23 3 0.736 2.209 0.000 -2.946 0.000 0.000 181 | 24 8 7 22 3 0.736 2.209 0.000 -2.946 0.000 0.000 182 | 8 7 6 3 3 16.736 -16.736 0.000 0.000 0.000 0.000 183 | 184 | 185 | -------------------------------------------------------------------------------- /DES/ITP/N-ethyl-N,N-dimethylethanolammonium_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; N-ethyl-N,N-dimethylethanolammonium 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ atomtypes ] 18 | ; type mass charge ptype sigma(nm) epsilon(kj/mol) 19 | CT 12.011 -0.47 A 3.50000E-01 2.76144E-01 20 | HT 1.008 0.436 A 2.50000E-01 1.25520E-01 21 | CG 12.011 -0.081 A 3.50000E-01 2.76144E-01 22 | HG 1.008 0.109 A 2.50000E-01 1.25520E-01 23 | CA 12.011 -0.053 A 3.50000E-01 2.76144E-01 24 | HA 1.008 0.144 A 2.50000E-01 1.25520E-01 25 | CS 12.011 -0.317 A 3.50000E-01 2.76144E-01 26 | HS 1.008 0.106 A 2.50000E-01 1.25520E-01 27 | CK 12.011 -0.119 A 3.50000E-01 2.76144E-01 28 | HK 1.008 0.143 A 2.50000E-01 1.25520E-01 29 | OH 15.999 -0.237 A 3.12000E-01 7.11280E-01 30 | HO 1.008 0.191 A 0.00000E+00 0.00000E+00 31 | N 14.007 -0.581 A 3.25000E-01 7.11280E-01 32 | 33 | 34 | -------------------------------------------------------------------------------- /DES/ITP/acetamide_DES.itp: -------------------------------------------------------------------------------- 1 | ; acetamide 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ moleculetype ] 18 | ; name nrexcl 19 | HBD 3 20 | 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass 24 | 1 opls_800 1 HBD C00 1 25 | 2 opls_801 1 HBD C01 1 26 | 3 opls_802 1 HBD N02 1 27 | 4 opls_803 1 HBD O03 1 28 | 5 opls_804 1 HBD H04 1 29 | 6 opls_804 1 HBD H05 1 30 | 7 opls_804 1 HBD H06 1 31 | 8 opls_807 1 HBD H07 1 32 | 9 opls_807 1 HBD H08 1 33 | 34 | 35 | [ bonds ] 36 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 37 | 2 1 1 0.1522 265265.600 38 | 3 2 1 0.1335 410032.000 39 | 4 2 1 0.1229 476976.000 40 | 5 1 1 0.1090 284512.000 41 | 6 1 1 0.1090 284512.000 42 | 7 1 1 0.1090 284512.000 43 | 8 3 1 0.1010 363171.200 44 | 9 3 1 0.1010 363171.200 45 | 46 | 47 | [ angles ] 48 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 49 | 1 2 3 1 116.600 585.760 50 | 1 2 4 1 120.400 669.440 51 | 2 1 5 1 109.500 292.880 52 | 2 1 6 1 109.500 292.880 53 | 2 1 7 1 109.500 292.880 54 | 2 3 8 1 119.800 292.880 55 | 2 3 9 1 119.800 292.880 56 | 6 1 7 1 107.800 276.144 57 | 5 1 6 1 107.800 276.144 58 | 3 2 4 1 122.900 669.440 59 | 8 3 9 1 120.000 292.880 60 | 5 1 7 1 107.800 276.144 61 | 62 | 63 | [ dihedrals ] 64 | ; IMPROPER DIHEDRAL ANGLES 65 | ; ai aj ak al func deg k(kj mol-1) mp 66 | 9 3 2 8 4 180.000 10.460 2 67 | 4 2 1 3 4 180.000 43.932 2 68 | 69 | 70 | [ dihedrals ] 71 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 72 | 8 3 2 1 3 20.502 0.000 -20.502 0.000 0.000 0.000 73 | 9 3 2 1 3 20.502 0.000 -20.502 0.000 0.000 0.000 74 | 9 3 2 4 3 20.502 0.000 -20.502 0.000 0.000 0.000 75 | 8 3 2 4 3 20.502 0.000 -20.502 0.000 0.000 0.000 76 | 5 1 2 3 3 0.000 0.000 0.000 0.000 0.000 0.000 77 | 6 1 2 3 3 0.000 0.000 0.000 0.000 0.000 0.000 78 | 7 1 2 3 3 0.000 0.000 0.000 0.000 0.000 0.000 79 | 5 1 2 4 3 0.000 0.000 0.000 0.000 0.000 0.000 80 | 6 1 2 4 3 0.000 0.000 0.000 0.000 0.000 0.000 81 | 7 1 2 4 3 0.000 0.000 0.000 0.000 0.000 0.000 82 | 83 | 84 | -------------------------------------------------------------------------------- /DES/ITP/acetamide_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; acetamide 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ atomtypes ] 18 | ; type mass charge ptype sigma(nm) epsilon(kj/mol) 19 | opls_800 12.011 -0.509 A 3.50000E-01 2.76144E-01 20 | opls_801 12.011 0.713 A 3.55000E-01 2.92880E-01 21 | opls_802 14.007 -0.493 A 3.25000E-01 7.11280E-01 22 | opls_803 15.999 -0.631 A 2.96000E-01 8.78640E-01 23 | opls_804 1.008 0.168 A 2.50000E-01 1.25520E-01 24 | opls_807 1.008 0.208 A 0.00000E+00 0.00000E+00 25 | 26 | 27 | -------------------------------------------------------------------------------- /DES/ITP/choline_DES.itp: -------------------------------------------------------------------------------- 1 | ; Choline cation [Chol] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | CHOL 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 CS 1 CHOL CS 1 -0.131 12.011 21 | 2 HS 1 CHOL HS 1 0.068 1.008 22 | 3 HS 1 CHOL HS 1 0.068 1.008 23 | 4 NA 1 CHOL NA 1 0.791 14.007 24 | 5 CW 1 CHOL CW 1 0.132 12.011 25 | 6 HW 1 CHOL HW 1 0.034 1.008 26 | 7 HW 1 CHOL HW 1 0.034 1.008 27 | 8 OY 1 CHOL OY 1 -0.468 15.999 28 | 9 HY 1 CHOL HY 1 0.275 1.008 29 | 10 CA 1 CHOL CA 1 -0.100 12.011 30 | 11 HA 1 CHOL HA 1 0.033 1.008 31 | 12 HA 1 CHOL HA 1 0.033 1.008 32 | 13 HA 1 CHOL HA 1 0.033 1.008 33 | 14 CA 1 CHOL CA 1 -0.100 12.011 34 | 15 HA 1 CHOL HA 1 0.033 1.008 35 | 16 HA 1 CHOL HA 1 0.033 1.008 36 | 17 HA 1 CHOL HA 1 0.033 1.008 37 | 18 CA 1 CHOL CA 1 -0.100 12.011 38 | 19 HA 1 CHOL HA 1 0.033 1.008 39 | 20 HA 1 CHOL HA 1 0.033 1.008 40 | 21 HA 1 CHOL HA 1 0.033 1.008 41 | 42 | [ bonds ] 43 | ; ai aj funct c0(nm) c1(kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 44 | 11 10 1 0.1099 284512.000 ; 1.0990 340 HA-CA 45 | 12 10 1 0.1099 284512.000 ; 1.0990 340 HA-CA 46 | 13 10 1 0.1099 284512.000 ; 1.0990 340 HA-CA 47 | 15 14 1 0.1099 284512.000 ; 1.0990 340 HA-CA 48 | 16 14 1 0.1099 284512.000 ; 1.0990 340 HA-CA 49 | 17 14 1 0.1099 284512.000 ; 1.0990 340 HA-CA 50 | 19 18 1 0.1099 284512.000 ; 1.0990 340 HA-CA 51 | 20 18 1 0.1099 284512.000 ; 1.0990 340 HA-CA 52 | 21 18 1 0.1099 284512.000 ; 1.0990 340 HA-CA 53 | 10 4 1 0.1498 410032.000 ; 1.4980 490 CA-NA 54 | 14 4 1 0.1498 410032.000 ; 1.4980 490 CA-NA 55 | 18 4 1 0.1498 410032.000 ; 1.4980 490 CA-NA 56 | 4 1 1 0.1516 410032.000 ; 1.5160 490 NA-CS 57 | 1 2 1 0.10805 284512.000 ; 1.0805 340 CS-HS 58 | 1 3 1 0.10805 284512.000 ; 1.0805 340 CS-HS 59 | 1 5 1 0.1521 265265.600 ; 1.5210 317 CS-CW 60 | 5 6 1 0.1085 284512.000 ; 1.0850 340 CW-HW 61 | 5 7 1 0.1085 284512.000 ; 1.0850 340 CW-HW 62 | 5 8 1 0.1395 376560.000 ; 1.3950 450 CW-OY 63 | 8 9 1 0.0949 462750.400 ; 0.9490 553 OY-HY 64 | 65 | [ angles ] 66 | ; ai aj ak funct c0(deg) c1(kj mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 67 | 11 10 12 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 68 | 11 10 13 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 69 | 12 10 13 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 70 | 15 14 16 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 71 | 15 14 17 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 72 | 16 14 17 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 73 | 19 18 20 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 74 | 19 18 21 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 75 | 20 18 21 1 110.01 292.8800 ; 110.01 35.0 HA-CA-HA 76 | 11 10 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 77 | 12 10 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 78 | 13 10 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 79 | 15 14 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 80 | 16 14 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 81 | 17 14 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 82 | 19 18 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 83 | 20 18 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 84 | 21 18 4 1 108.90 292.8800 ; 108.90 35.0 HA-CA-NA 85 | 10 4 1 1 110.20 433.4624 ; 110.20 51.8 CA-NA-CS 86 | 14 4 1 1 110.20 433.4624 ; 110.20 51.8 CA-NA-CS 87 | 18 4 1 1 110.20 433.4624 ; 110.20 51.8 CA-NA-CS 88 | 4 1 2 1 106.40 292.8800 ; 106.40 35.0 NA-CS-HS 89 | 4 1 3 1 106.40 292.8800 ; 106.40 35.0 NA-CS-HS 90 | 4 1 5 1 116.60 585.7600 ; 116.60 70.0 NA-CS-CW 91 | 1 5 6 1 108.30 292.8800 ; 108.30 35.0 CS-CW-HW 92 | 1 5 7 1 108.30 292.8800 ; 108.30 35.0 CS-CW-HW 93 | 1 5 8 1 109.60 669.4400 ; 109.60 80.0 CS-CW-OY 94 | 2 1 5 1 109.30 292.8800 ; 109.30 35.0 HS-CS-CW 95 | 3 1 5 1 109.30 292.8800 ; 109.30 35.0 HS-CS-CW 96 | 6 5 8 1 111.60 292.8800 ; 111.60 35.0 HW-CW-OY 97 | 7 5 8 1 111.60 292.8800 ; 111.60 35.0 HW-CW-OY 98 | 5 8 9 1 110.90 292.8800 ; 110.90 35.0 CW-OY-HY 99 | 10 4 14 1 108.73 460.2400 ; 108.73 55.0 CA-NA-CA 100 | 10 4 18 1 108.73 460.2400 ; 108.73 55.0 CA-NA-CA 101 | 14 4 18 1 108.73 460.2400 ; 108.73 55.0 CA-NA-CA 102 | 2 1 3 1 108.60 292.8800 ; 108.60 35.0 HS-CS-HS 103 | 6 5 7 1 107.40 292.8800 ; 107.40 35.0 HW-CW-Hw 104 | 105 | [ dihedrals ] 106 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 107 | 5 1 4 10 5 0.4184 2.30120 2.71960 0.0000 ; 0.100 0.550 0.650 0.000 CW-CS-NA-CA 108 | 5 1 4 14 5 0.4184 2.30120 2.71960 0.0000 ; 0.100 0.550 0.650 0.000 CW-CS-NA-CA 109 | 5 1 4 18 5 0.4184 2.30120 2.71960 0.0000 ; 0.100 0.550 0.650 0.000 CW-CS-NA-CA 110 | 10 4 14 15 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 111 | 10 4 14 16 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 112 | 10 4 14 17 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 113 | 10 4 18 19 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 114 | 10 4 18 20 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 115 | 10 4 18 21 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 116 | 14 4 10 11 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 117 | 14 4 10 12 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 118 | 14 4 10 13 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 119 | 14 4 18 19 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 120 | 14 4 18 20 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 121 | 14 4 18 21 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 122 | 18 4 10 11 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 123 | 18 4 10 12 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 124 | 18 4 10 13 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 125 | 18 4 14 15 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 126 | 18 4 14 16 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 127 | 18 4 14 17 5 0.0000 0.00000 3.45180 0.0000 ; 0.000 0.000 0.825 0.000 CA-NA-CA-HA 128 | 1 4 10 11 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 129 | 1 4 10 12 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 130 | 1 4 10 13 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 131 | 1 4 14 15 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 132 | 1 4 14 16 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 133 | 1 4 14 17 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 134 | 1 4 18 19 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 135 | 1 4 18 20 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 136 | 1 4 18 21 5 0.0000 0.00000 3.93296 0.0000 ; 0.000 0.000 0.940 0.000 CS-NA-CA-HA 137 | 2 1 4 10 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 138 | 2 1 4 14 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 139 | 2 1 4 18 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 140 | 3 1 4 10 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 141 | 3 1 4 14 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 142 | 3 1 4 18 5 0.0000 4.18400 2.92880 0.0000 ; 0.000 1.000 0.700 0.000 HS-CS-NA-CA 143 | 8 5 1 4 5 -25.1040 -20.92000 13.38880 0.0000 ; -6.000 -5.000 3.200 0.000 OY-CW-CS-NA 144 | 8 5 1 2 5 -2.0920 -10.46000 1.04600 0.0000 ; -0.500 -2.500 0.250 0.000 OY-CW-CS-HS 145 | 8 5 1 3 5 -2.0920 -10.46000 1.04600 0.0000 ; -0.500 -2.500 0.250 0.000 OY-CW-CS-HS 146 | 6 5 1 4 5 -25.1040 -29.28800 3.13800 0.0000 ; -6.000 -7.000 0.750 0.000 HW-CW-CS-NA 147 | 7 5 1 4 5 -25.1040 -29.28800 3.13800 0.0000 ; -6.000 -7.000 0.750 0.000 HW-CW-CS-NA 148 | 6 5 1 2 5 25.1040 -12.55200 8.36800 0.0000 ; 6.000 -3.000 2.000 0.000 HW-CW-CS-HS 149 | 6 5 1 3 5 25.1040 -12.55200 8.36800 0.0000 ; 6.000 -3.000 2.000 0.000 HW-CW-CS-HS 150 | 7 5 1 2 5 25.1040 -12.55200 8.36800 0.0000 ; 6.000 -3.000 2.000 0.000 HW-CW-CS-HS 151 | 7 5 1 3 5 25.1040 -12.55200 8.36800 0.0000 ; 6.000 -3.000 2.000 0.000 HW-CW-CS-HS 152 | 9 8 5 1 5 -1.4895 -0.72802 1.46440 0.0000 ; -0.356 -0.174 0.350 0.000 HY-OY-CW-CS 153 | 9 8 5 6 5 -12.552 4.18400 -8.36800 0.0000 ; -3.000 1.000 -2.000 0.000 HY-OY-CW-HW 154 | 9 8 5 7 5 -12.552 4.18400 -8.36800 0.0000 ; -3.000 1.000 -2.000 0.000 HY-OY-CW-HW 155 | 10 4 14 18 5 0.000 8.36800 0.00000 0.0000 ; 0.000 2.000 0.000 0.000 CA-NA-CA-CA improper 156 | 1 4 10 14 5 0.000 8.36800 0.00000 0.0000 ; 0.000 2.000 0.000 0.000 CS-NA-CA-CA improper 157 | 1 4 10 18 5 0.000 8.36800 0.00000 0.0000 ; 0.000 2.000 0.000 0.000 CS-NA-CA-CA improper 158 | 1 4 14 18 5 0.000 8.36800 0.00000 0.0000 ; 0.000 2.000 0.000 0.000 CS-NA-CA-CA improper 159 | 160 | -------------------------------------------------------------------------------- /DES/ITP/choline_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Choline cation [Chol] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma (Ang.) epsilon (kcal/mol) 16 | CS 12.011 -0.131 A 0.3500 0.276144 ; 3.50 0.066 17 | HS 1.008 0.068 A 0.2600 0.125520 ; 2.60 0.030 18 | NA 14.007 0.791 A 0.3250 0.711280 ; 3.25 0.170 19 | CA 12.011 -0.100 A 0.3500 0.276144 ; 3.50 0.066 20 | CW 12.011 0.132 A 0.3500 0.276144 ; 3.50 0.066 21 | OY 15.999 -0.468 A 0.3070 0.711280 ; 3.07 0.170 22 | HA 1.008 0.033 A 0.2500 0.125520 ; 2.50 0.030 23 | HW 1.008 0.034 A 0.2200 0.125520 ; 2.20 0.030 24 | HY 1.008 0.275 A 0.0000 0.000000 ; 0.00 0.000 25 | 26 | -------------------------------------------------------------------------------- /DES/ITP/cl_DES.itp: -------------------------------------------------------------------------------- 1 | ; Chlorine anion [cl] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | Cl 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 Cl 1 Cl Cl 1 -0.800 35.45 21 | 22 | -------------------------------------------------------------------------------- /DES/ITP/cl_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Chlorine anion [cl] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma (Ang.) epsilon (kcal/mol) 16 | Cl 35.45 -0.800 A 0.377 0.619232 ; 3.77 0.1480 17 | -------------------------------------------------------------------------------- /DES/ITP/ethgly_DES.itp: -------------------------------------------------------------------------------- 1 | ; Ethylene Glycol HBD [ETGLY] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | ETGLY 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 CG 1 ETGLY C01 1 0.116 12.011 21 | 2 HG 1 ETGLY H02 1 0.048 1.008 22 | 3 HG 1 ETGLY H03 1 0.048 1.008 23 | 4 CG 1 ETGLY C04 1 0.116 12.011 24 | 5 HG 1 ETGLY H05 1 0.048 1.008 25 | 6 HG 1 ETGLY H06 1 0.048 1.008 26 | 7 OG 1 ETGLY O07 1 -0.560 15.999 27 | 8 HO 1 ETGLY H08 1 0.348 1.008 28 | 9 OG 1 ETGLY O09 1 -0.560 15.999 29 | 10 HO 1 ETGLY H10 1 0.348 1.008 30 | 31 | [ bonds ] 32 | ; ai aj funct c0 (nm) c1 (kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 33 | 1 4 1 0.1529 224262.000 ; 1.529 268 CG-CG 34 | 1 2 1 0.1090 284512.000 ; 1.090 340 CG-HG 35 | 1 3 1 0.1090 284512.000 ; 1.090 340 CG-HG 36 | 4 5 1 0.1090 284512.000 ; 1.090 340 CG-HG 37 | 4 6 1 0.1090 284512.000 ; 1.090 340 CG-HG 38 | 1 9 1 0.1430 267776.000 ; 1.410 320 CG-OG 39 | 4 7 1 0.1430 267776.000 ; 1.410 320 CG-OG 40 | 7 8 1 0.0945 462750.400 ; 0.945 553 OG-HO 41 | 9 10 1 0.0945 462750.400 ; 0.945 553 OG-HO 42 | 43 | [ angles ] 44 | ; ai aj ak funct c0 (deg) c1 (kJ mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 45 | 1 4 7 1 108.0 418.400 ; 108.0 50.0 CG-CG-OG 46 | 4 1 9 1 108.0 418.400 ; 108.0 50.0 CG-CG-OG 47 | 1 4 5 1 110.7 313.800 ; 110.7 37.5 CG-CG-HG 48 | 1 4 6 1 110.7 313.800 ; 110.7 37.5 CG-CG-HG 49 | 4 1 2 1 110.7 313.800 ; 110.7 37.5 CG-CG-HG 50 | 4 1 3 1 110.7 313.800 ; 110.7 37.5 CG-CG-HG 51 | 2 1 3 1 107.8 276.140 ; 107.8 33.0 HG-CG-HG 52 | 5 4 6 1 107.8 276.140 ; 107.8 33.0 HG-CG-HG 53 | 2 1 9 1 109.5 292.880 ; 109.5 35.0 HG-CG-OG 54 | 3 1 9 1 109.5 292.880 ; 109.5 35.0 HG-CG-OG 55 | 5 4 7 1 109.5 292.880 ; 109.5 35.0 HG-CG-OG 56 | 6 4 7 1 109.5 292.880 ; 109.5 35.0 HG-CG-OG 57 | 4 7 8 1 108.5 460.240 ; 108.5 55.0 CG-OG-HO 58 | 1 9 10 1 108.5 460.240 ; 108.5 55.0 CG-OG-HO 59 | 60 | [ dihedrals ] 61 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 62 | 9 1 4 7 5 16.264 -4.987 13.414 0.000 ; 3.887 -1.192 3.206 0.000 OG-CG-CG-OG 63 | 1 4 7 8 5 1.727 -3.156 4.303 0.000 ; 0.413 -0.754 1.028 0.000 CG-CG-OG-HO 64 | 4 1 9 10 5 1.727 -3.156 4.303 0.000 ; 0.413 -0.754 1.028 0.000 CG-CG-OG-HO 65 | 66 | [ exclusions ] 67 | 8 9 68 | 7 10 69 | 70 | -------------------------------------------------------------------------------- /DES/ITP/ethgly_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Ethylene Glycol HBD [ETGLY] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma(Ang.) epsilon(kcal/mol) 16 | CG 12.011 0.116 A 0.350 0.276144 ; 3.50 0.1155 17 | HG 1.008 0.048 A 0.250 0.125520 ; 2.50 0.0525 18 | OG 15.999 -0.560 A 0.300 0.711280 ; 3.00 0.2975 19 | HO 1.008 0.348 A 0.000 0.000000 ; 0.00 0.0000 20 | 21 | -------------------------------------------------------------------------------- /DES/ITP/ethylammonium_DES.itp: -------------------------------------------------------------------------------- 1 | ; ethylammonium 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ moleculetype ] 18 | ; name nrexcl 19 | MOL 3 20 | 21 | 22 | [ atoms ] 23 | ; nr type resnr residue atom cgnr charge mass 24 | 1 CT 1 MOL C00 1 25 | 2 CA 1 MOL C01 1 26 | 3 N 1 MOL N02 1 27 | 4 HN 1 MOL H03 1 28 | 5 HN 1 MOL H04 1 29 | 6 HN 1 MOL H05 1 30 | 7 HT 1 MOL H06 1 31 | 8 HT 1 MOL H07 1 32 | 9 HT 1 MOL H08 1 33 | 10 HA 1 MOL H09 1 34 | 11 HA 1 MOL H0A 1 35 | 36 | 37 | [ bonds ] 38 | ; ai aj func c0(nm) c1(kj mol-1 nm-2) 39 | 2 1 1 0.1529 224262.400 40 | 3 2 1 0.1471 307105.600 41 | 4 3 1 0.1010 363171.200 42 | 5 3 1 0.1010 363171.200 43 | 6 3 1 0.1010 363171.200 44 | 7 1 1 0.1090 284512.000 45 | 8 1 1 0.1090 284512.000 46 | 9 1 1 0.1090 284512.000 47 | 10 2 1 0.1090 284512.000 48 | 11 2 1 0.1090 284512.000 49 | 50 | 51 | [ angles ] 52 | ; ai aj ak func c0(nm) c1(kj mol-1 nm-2) 53 | 1 2 3 1 111.200 669.440 54 | 2 3 4 1 107.640 269.031 55 | 2 3 5 1 107.640 269.031 56 | 2 3 6 1 107.640 269.031 57 | 2 1 7 1 110.700 313.800 58 | 2 1 8 1 110.700 313.800 59 | 2 1 9 1 110.700 313.800 60 | 1 2 10 1 110.700 313.800 61 | 1 2 11 1 110.700 313.800 62 | 7 1 8 1 107.800 276.144 63 | 4 3 6 1 109.500 364.845 64 | 5 3 6 1 109.500 364.845 65 | 10 2 11 1 107.800 276.144 66 | 3 2 10 1 109.500 292.880 67 | 3 2 11 1 109.500 292.880 68 | 7 1 9 1 107.800 276.144 69 | 4 3 5 1 109.500 364.845 70 | 8 1 9 1 107.800 276.144 71 | 72 | 73 | [ dihedrals ] 74 | ; ai aj ak al func c0 c1 c2 c3 c4 c5 75 | 4 3 2 1 3 0.726 2.178 0.000 -2.904 -0.000 0.000 76 | 6 3 2 1 3 0.726 2.178 0.000 -2.904 -0.000 0.000 77 | 5 3 2 1 3 0.726 2.178 0.000 -2.904 -0.000 0.000 78 | 10 2 1 9 3 0.628 1.883 0.000 -2.510 -0.000 0.000 79 | 11 2 1 7 3 0.628 1.883 0.000 -2.510 -0.000 0.000 80 | 10 2 1 7 3 0.628 1.883 0.000 -2.510 -0.000 0.000 81 | 11 2 1 8 3 0.628 1.883 0.000 -2.510 -0.000 0.000 82 | 11 2 1 9 3 0.628 1.883 0.000 -2.510 -0.000 0.000 83 | 10 2 1 8 3 0.628 1.883 0.000 -2.510 -0.000 0.000 84 | 7 1 2 3 3 0.803 2.410 0.000 -3.213 -0.000 0.000 85 | 9 1 2 3 3 0.803 2.410 0.000 -3.213 -0.000 0.000 86 | 8 1 2 3 3 0.803 2.410 0.000 -3.213 -0.000 0.000 87 | 10 2 3 6 3 0.546 1.638 0.000 -2.184 -0.000 0.000 88 | 10 2 3 4 3 0.546 1.638 0.000 -2.184 -0.000 0.000 89 | 11 2 3 5 3 0.546 1.638 0.000 -2.184 -0.000 0.000 90 | 10 2 3 5 3 0.546 1.638 0.000 -2.184 -0.000 0.000 91 | 11 2 3 4 3 0.546 1.638 0.000 -2.184 -0.000 0.000 92 | 11 2 3 6 3 0.546 1.638 0.000 -2.184 -0.000 0.000 93 | 94 | 95 | -------------------------------------------------------------------------------- /DES/ITP/ethylammonium_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; ethylammonium 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | 17 | [ atomtypes ] 18 | ; type mass charge ptype sigma(nm) epsilon(kj/mol) 19 | CT 12.011 -0.248 A 3.50000E-01 2.76144E-01 20 | HT 1.008 0.146 A 2.50000E-01 1.25520E-01 21 | CA 12.011 -0.44 A 3.50000E-01 2.76144E-01 22 | HA 1.008 0.15 A 2.50000E-01 1.25520E-01 23 | N 14.007 -0.205 A 3.25000E-01 7.11280E-01 24 | HN 1.008 0.385 A 0.00000E+00 0.00000E+00 25 | 26 | 27 | -------------------------------------------------------------------------------- /DES/ITP/glycerol_DES.itp: -------------------------------------------------------------------------------- 1 | ; Glycerol HBD [GLY] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | GLY 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 CM 1 GLY CM 1 0.1420 12.011 21 | 2 OM 1 GLY OM 2 -0.5447 15.999 22 | 3 CB 1 GLY CB 3 0.1600 12.011 23 | 4 CB 1 GLY CB 4 0.1600 12.011 24 | 5 HM 1 GLY HM 2 0.2912 1.008 25 | 6 HZ 1 GLY HZ 1 0.0221 1.008 26 | 7 HC 1 GLY HC 3 0.0637 1.008 27 | 8 HC 1 GLY HC 3 0.0637 1.008 28 | 9 HC 1 GLY HC 4 0.0637 1.008 29 | 10 HC 1 GLY HC 4 0.0637 1.008 30 | 11 OH 1 GLY OH 5 -0.5470 15.999 31 | 12 OH 1 GLY OH 6 -0.5470 15.999 32 | 13 HO 1 GLY HO 5 0.3043 1.008 33 | 14 HO 1 GLY HO 6 0.3043 1.008 34 | 35 | [ bonds ] 36 | ; ai aj funct c0(nm) c1(kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 37 | 2 1 1 0.1410 267776.000 ; 1.410 320 OM-CM 38 | 3 1 1 0.1529 224262.400 ; 1.529 268 CB-CM 39 | 4 1 1 0.1529 224262.400 ; 1.529 268 CB-CM 40 | 5 2 1 0.0945 462750.000 ; 0.945 553 HM-OM 41 | 6 1 1 0.1090 284512.000 ; 1.090 340 HZ-CM 42 | 7 3 1 0.1090 284512.000 ; 1.090 340 HC-CB 43 | 8 3 1 0.1090 284512.000 ; 1.090 340 HC-CB 44 | 9 4 1 0.1090 284512.000 ; 1.090 340 HC-CB 45 | 10 4 1 0.1090 284512.000 ; 1.090 340 HC-CB 46 | 11 3 1 0.1410 267776.000 ; 1.410 320 OH-CB 47 | 12 4 1 0.1410 267776.000 ; 1.410 320 OH-CB 48 | 13 11 1 0.0945 462750.400 ; 0.945 553 HO-OH 49 | 14 12 1 0.0945 462750.400 ; 0.945 553 HO-OH 50 | 51 | [ angles ] 52 | ; ai aj ak funct c0(deg) c1(kj mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 53 | 2 1 3 1 109.5 418.4000 ; 109.5 50.00 OM-CM-CB 54 | 2 1 4 1 109.5 418.4000 ; 109.5 50.00 OM-CM-CB 55 | 1 2 5 1 108.5 460.2400 ; 108.5 55.00 CM-OM-HM 56 | 2 1 6 1 109.5 292.8800 ; 109.5 35.00 OM-CM-HZ 57 | 1 3 7 1 110.7 313.8000 ; 110.7 37.50 CM-CB-HC 58 | 1 3 8 1 110.7 313.8000 ; 110.7 37.50 CM-CB-HC 59 | 1 4 9 1 110.7 313.8000 ; 110.7 37.50 CM-CB-HC 60 | 1 4 10 1 110.7 313.8000 ; 110.7 37.50 CM-CB-HC 61 | 1 3 11 1 109.5 418.4000 ; 109.5 50.00 CM-CB-OH 62 | 1 4 12 1 109.5 418.4000 ; 109.5 50.00 CM-CB-OH 63 | 3 11 13 1 108.5 460.2400 ; 108.5 55.00 CB-OH-HO 64 | 4 12 14 1 108.5 460.2400 ; 108.5 55.00 CB-OH-HO 65 | 3 1 4 1 112.7 488.2728 ; 112.7 58.35 CB-CM-CB 66 | 3 1 6 1 110.7 313.8000 ; 110.7 37.50 CB-CM-HZ 67 | 4 1 6 1 110.7 313.8000 ; 110.7 37.50 CB-CM-HZ 68 | 7 3 8 1 107.8 276.1440 ; 107.8 33.00 HC-CB-HC 69 | 7 3 11 1 109.5 292.8800 ; 109.5 35.00 HC-CB-OH 70 | 8 3 11 1 109.5 292.8800 ; 109.5 35.00 HC-CB-OH 71 | 9 4 10 1 107.8 276.1440 ; 107.8 33.00 HC-CB-HC 72 | 9 4 12 1 109.5 292.8800 ; 109.5 35.00 HC-CB-OH 73 | 10 4 12 1 109.5 292.8800 ; 109.5 35.00 HC-CB-OH 74 | 75 | [ dihedrals ] 76 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 77 | 4 1 2 3 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 CB-CM-OM-CB improper 78 | 5 2 1 3 5 -1.4895 -0.7280 2.0585 0.0000 ; -0.356 -0.174 0.492 0.000 HM-OM-CM-CB 79 | 6 1 2 5 5 0.0000 0.0000 1.4728 0.0000 ; 0.000 0.000 0.352 0.000 HZ-CM-OM-HM 80 | 7 3 1 2 5 0.0000 0.0000 1.9581 0.0000 ; 0.000 0.000 0.468 0.000 HC-CB-CM-OM 81 | 8 3 1 2 5 0.0000 0.0000 1.9581 0.0000 ; 0.000 0.000 0.468 0.000 HC-CB-CM-OM 82 | 9 4 1 2 5 0.0000 0.0000 1.9581 0.0000 ; 0.000 0.000 0.468 0.000 HC-CB-CM-OM 83 | 10 4 1 2 5 0.0000 0.0000 1.9581 0.0000 ; 0.000 0.000 0.468 0.000 HC-CB-CM-OM 84 | 11 3 1 2 5 51.1871 0.0000 0.0000 0.0000 ; 12.234 0.000 0.000 0.000 OH-CB-CM-OM 85 | 12 4 1 2 5 51.1871 0.0000 0.0000 0.0000 ; 12.234 0.000 0.000 0.000 OH-CB-CM-OM 86 | 13 11 3 1 5 -1.4895 -0.7280 2.0585 0.0000 ; -0.356 -0.174 0.492 0.000 HO-OH-CB-CM 87 | 14 12 4 1 5 -1.4895 -0.7280 2.0585 0.0000 ; -0.356 -0.174 0.492 0.000 HO-OH-CB-CM 88 | 5 2 1 4 5 -1.4895 -0.7280 2.0585 0.0000 ; -0.356 -0.174 0.492 0.000 HM-OM-CM-CB 89 | 7 3 1 4 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HC-CB-CM-CB 90 | 8 3 1 4 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HC-CB-CM-CB 91 | 11 3 1 4 5 -6.4936 0.0000 0.0000 0.0000 ; -1.552 0.000 0.000 0.000 OH-CB-CM-CB 92 | 7 3 1 6 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HC-CB-CM-HZ 93 | 8 3 1 6 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HC-CB-CM-HZ 94 | 11 3 1 6 5 0.0000 0.0000 1.9581 0.0000 ; 0.000 0.000 0.468 0.000 OH-CB-CM-HZ 95 | 9 4 1 3 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HC-CB-CM-CB 96 | 10 4 1 3 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HC-CB-CM-CB 97 | 12 4 1 3 5 -6.4936 0.0000 0.0000 0.0000 ; -1.552 0.000 0.000 0.000 OH-CB-CM-CB 98 | 9 4 1 6 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HC-CB-CM-HZ 99 | 10 4 1 6 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HC-CB-CM-HZ 100 | 12 4 1 6 5 0.0000 0.0000 1.9581 0.0000 ; 0.000 0.000 0.468 0.000 OH-CB-CM-HZ 101 | 13 11 3 7 5 0.0000 0.0000 1.4728 0.0000 ; 0.000 0.000 0.352 0.000 HO-OH-CB-HC 102 | 13 11 3 8 5 0.0000 0.0000 1.4728 0.0000 ; 0.000 0.000 0.352 0.000 HO-OH-CB-HC 103 | 14 12 4 9 5 0.0000 0.0000 1.4728 0.0000 ; 0.000 0.000 0.352 0.000 HO-OH-CB-HC 104 | 14 12 4 10 5 0.0000 0.0000 1.4728 0.0000 ; 0.000 0.000 0.352 0.000 HO-OH-CB-HC 105 | 106 | [ exclusions ] 107 | 2 13 108 | 2 14 109 | 5 11 110 | 5 12 111 | 112 | -------------------------------------------------------------------------------- /DES/ITP/glycerol_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Glycerol HBD [GLY] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma(Ang.) epsilon(kcal/mol) 16 | CM 12.011 0.1420 A 0.350 0.607517 ; 3.50 0.1452 17 | OM 15.999 -0.5447 A 0.307 1.564816 ; 3.07 0.3740 18 | CB 12.011 0.1600 A 0.350 0.607517 ; 3.50 0.1452 19 | HM 1.008 0.2912 A 0.000 0.000000 ; 0.00 0.0000 20 | HZ 1.008 0.0221 A 0.250 0.276144 ; 2.50 0.0660 21 | HC 1.008 0.0637 A 0.250 0.276144 ; 2.50 0.0660 22 | OH 15.999 -0.5470 A 0.307 1.564816 ; 3.07 0.3740 23 | HO 1.008 0.3043 A 0.000 0.000000 ; 0.00 0.0000 24 | 25 | -------------------------------------------------------------------------------- /DES/ITP/levulinic_DES.itp: -------------------------------------------------------------------------------- 1 | ; Levulinic Acid HBD [LEV] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | lev 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 CB 1 lev C0A 1 0.416 12.011 21 | 2 OH 1 lev O0B 2 -0.424 15.999 22 | 3 HO 1 lev H0C 2 0.360 1.008 23 | 4 OB 1 lev O0D 3 -0.352 15.999 24 | 5 CZ 1 lev C0E 4 -0.096 12.011 25 | 6 HZ 1 lev H0F 4 0.048 1.008 26 | 7 HZ 1 lev H0G 4 0.048 1.008 27 | 8 CF 1 lev C0H 5 -0.096 12.011 28 | 9 HF 1 lev H0I 5 0.048 1.008 29 | 10 HF 1 lev H0J 5 0.048 1.008 30 | 11 CD 1 lev C0K 6 0.376 12.011 31 | 12 CT 1 lev C0L 7 -0.144 12.011 32 | 13 HT 1 lev H0M 7 0.048 1.008 33 | 14 HT 1 lev H0N 7 0.048 1.008 34 | 15 HT 1 lev H0O 7 0.048 1.008 35 | 16 OC 1 lev O0P 8 -0.376 15.999 36 | 37 | [ bonds ] 38 | ; ai aj funct c0(nm) c1(kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 39 | 2 1 1 0.1364 376560.0 ; 1.364 450 OH-CB 40 | 2 3 1 0.0945 462750.4 ; 0.945 553 OH-HO 41 | 4 1 1 0.1229 476976.0 ; 1.229 570 OB-CB 42 | 5 1 1 0.1522 265265.6 ; 1.522 317 CZ-CB 43 | 6 5 1 0.1090 284512.0 ; 1.090 340 HZ-CZ 44 | 7 5 1 0.1090 284512.0 ; 1.090 340 HZ-CZ 45 | 8 5 1 0.1529 224262.4 ; 1.529 268 CF-CZ 46 | 9 8 1 0.1090 284512.0 ; 1.090 340 HF-CF 47 | 10 8 1 0.1090 284512.0 ; 1.090 340 HF-CF 48 | 11 8 1 0.1522 265265.6 ; 1.522 317 CD-CF 49 | 12 11 1 0.1522 265265.6 ; 1.522 317 CT-CD 50 | 13 12 1 0.1090 284512.0 ; 1.090 340 HT-CT 51 | 14 12 1 0.1090 284512.0 ; 1.090 340 HT-CT 52 | 15 12 1 0.1090 284512.0 ; 1.090 340 HT-CT 53 | 16 11 1 0.1229 476976.0 ; 1.229 570 OC-CD 54 | 55 | [ angles ] 56 | ; ai aj ak funct c0(deg) c1(kj mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 57 | 1 2 3 1 113.0 292.880 ; 113.0 35.0 CB-OH-HO 58 | 2 1 4 1 121.0 669.440 ; 121.0 80.0 OH-CB-OB 59 | 2 1 5 1 108.0 585.760 ; 108.0 70.0 OH-CB-CZ 60 | 1 5 6 1 109.5 292.880 ; 109.5 35.0 CB-CZ-HZ 61 | 1 5 7 1 109.5 292.880 ; 109.5 35.0 CB-CZ-HZ 62 | 1 5 8 1 111.1 527.184 ; 111.1 63.0 CB-CZ-CF 63 | 5 8 9 1 110.7 313.800 ; 110.7 37.5 CZ-CF-HF 64 | 5 8 10 1 110.7 313.800 ; 110.7 37.5 CZ-CF-HF 65 | 5 8 11 1 111.1 527.184 ; 111.1 63.0 CZ-CF-CD 66 | 8 11 12 1 116.0 585.760 ; 116.0 70.0 CF-CD-CT 67 | 11 12 13 1 109.5 292.880 ; 109.5 35.0 CD-CT-HT 68 | 11 12 14 1 109.5 292.880 ; 109.5 35.0 CD-CT-HT 69 | 11 12 15 1 109.5 292.880 ; 109.5 35.0 CD-CT-HT 70 | 8 11 16 1 120.4 669.440 ; 120.4 80.0 CF-CD-OC 71 | 4 1 5 1 120.4 669.440 ; 120.4 80.0 OB-CB-CZ 72 | 6 5 7 1 107.8 276.144 ; 107.8 33.0 HZ-CZ-HZ 73 | 6 5 8 1 110.7 313.800 ; 110.7 37.5 HZ-CZ-CF 74 | 7 5 8 1 110.7 313.800 ; 107.8 33.0 HZ-CZ-HZ 75 | 9 8 10 1 107.8 276.144 ; 107.8 33.0 HF-CF-HF 76 | 9 8 11 1 109.5 292.880 ; 109.5 35.0 HF-CF-CD 77 | 10 8 11 1 109.5 292.880 ; 109.5 35.0 HF-CF-CD 78 | 12 11 16 1 120.4 669.440 ; 120.4 80.0 CT-CD-OC 79 | 13 12 14 1 107.8 276.144 ; 107.8 33.0 HT-CT-HT 80 | 13 12 15 1 107.8 276.144 ; 107.8 33.0 HT-CT-HT 81 | 14 12 15 1 107.8 276.144 ; 107.8 33.0 HT-CT-HT 82 | 83 | [ dihedrals ] 84 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 85 | 4 1 2 3 5 0.0000 23.0120 0.0000 0.0000 ; 0.000 5.500 0.000 0.000 OB-CB-OH-HO 86 | 5 1 2 3 5 6.2760 23.0120 0.0000 0.0000 ; 1.500 5.500 0.000 0.000 CZ-CB-OH-HO 87 | 6 5 1 4 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HZ-CZ-CB-OB 88 | 7 5 1 4 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HZ-CZ-CB-OB 89 | 8 5 1 4 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 CF-CZ-CB-OB 90 | 9 8 5 1 5 0.0000 0.0000 -0.4184 0.0000 ; 0.000 0.000 -0.100 0.000 HF-CF-CZ-CB 91 | 10 8 5 1 5 0.0000 0.0000 -0.4184 0.0000 ; 0.000 0.000 -0.100 0.000 HF-CF-CZ-CB 92 | 11 8 5 1 5 -2.3012 0.0000 4.1840 0.0000 ; -0.550 0.000 1.000 0.000 CD-CF-CZ-CB 93 | 12 11 8 5 5 6.0835 -0.6025 -3.2426 0.0000 ; 1.454 -0.144 -0.775 0.000 CT-CD-CF-CZ 94 | 13 12 11 8 5 0.0000 0.0000 1.1506 0.0000 ; 0.000 0.000 0.275 0.000 HT-CT-CD-CF 95 | 14 12 11 8 5 0.0000 0.0000 1.1506 0.0000 ; 0.000 0.000 0.275 0.000 HT-CT-CD-CF 96 | 15 12 11 8 5 0.0000 0.0000 1.1506 0.0000 ; 0.000 0.000 0.275 0.000 HT-CT-CD-CF 97 | 16 11 8 5 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OC-CD-CF-CZ 98 | 6 5 1 2 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HZ-CZ-CB-OH 99 | 7 5 1 4 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HZ-CZ-CB-OH 100 | 8 5 1 2 5 4.1840 2.2845 1.8828 0.0000 ; 1.000 0.546 0.450 0.000 CF-CZ-CB-OH 101 | 9 8 5 6 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HF-CF-CZ-HZ 102 | 10 8 5 6 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HF-CF-CZ-HZ 103 | 11 8 5 6 5 0.0000 0.0000 -0.4184 0.0000 ; 0.000 0.000 -0.100 0.000 CD-CF-CZ-HZ 104 | 9 8 5 7 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HF-CF-CZ-HZ 105 | 10 8 5 7 5 0.0000 0.0000 1.2552 0.0000 ; 0.000 0.000 0.300 0.000 HF-CF-CZ-HZ 106 | 11 8 5 7 5 0.0000 0.0000 -0.4184 0.0000 ; 0.000 0.000 -0.100 0.000 CD-CF-CZ-HZ 107 | 12 11 8 9 5 0.0000 0.0000 1.1506 0.0000 ; 0.000 0.000 0.275 0.000 CT-CD-CF-HF 108 | 16 11 8 9 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OC-CD-CF-HF 109 | 12 11 8 10 5 0.0000 0.0000 1.1506 0.0000 ; 0.000 0.000 0.275 0.000 CT-CD-CF-HF 110 | 16 11 8 10 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OC-CD-CF-HF 111 | 16 11 12 13 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OC-CD-CT-HT 112 | 16 11 12 14 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OC-CD-CT-HT 113 | 16 11 12 15 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OC-CD-CT-HT 114 | 115 | -------------------------------------------------------------------------------- /DES/ITP/levulinic_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Levulinic Acid HBD [LEV] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma(Ang.) epsilon(kcal/mol) 16 | CB 12.011 0.416 A 0.375 0.527184 ; 3.75 0.1260 17 | OH 15.999 -0.424 A 0.300 0.853536 ; 3.00 0.2040 18 | HO 1.008 0.360 A 0.000 0.000000 ; 0.00 0.0000 19 | OB 15.999 -0.352 A 0.296 1.054368 ; 2.96 0.2520 20 | CZ 12.011 -0.096 A 0.350 0.331373 ; 3.50 0.0792 21 | HZ 1.008 0.048 A 0.250 0.150624 ; 2.50 0.0360 22 | CF 12.011 -0.096 A 0.350 0.331373 ; 3.50 0.0792 23 | HF 1.008 0.048 A 0.250 0.150624 ; 2.50 0.0360 24 | CD 12.011 0.376 A 0.375 0.527184 ; 3.75 0.1260 25 | CT 12.011 -0.144 A 0.350 0.331373 ; 3.50 0.0792 26 | HT 1.008 0.048 A 0.250 0.150624 ; 2.50 0.0360 27 | OC 12.011 -0.376 A 0.296 1.054368 ; 2.96 0.2520 28 | 29 | -------------------------------------------------------------------------------- /DES/ITP/malonic_DES.itp: -------------------------------------------------------------------------------- 1 | ; Malonic Acid HBD [MAL] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | MAL 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 CD 1 MAL C01 1 0.416 12.011 21 | 2 CT 1 MAL C02 2 -0.096 12.011 22 | 3 HC 1 MAL H03 2 0.048 1.008 23 | 4 HC 1 MAL H04 2 0.048 1.008 24 | 5 CD 1 MAL C05 3 0.416 12.011 25 | 6 OD 1 MAL O06 4 -0.352 15.999 26 | 7 OD 1 MAL O07 5 -0.352 15.999 27 | 8 OH 1 MAL O08 6 -0.424 15.999 28 | 9 OH 1 MAL O09 7 -0.424 15.999 29 | 10 HO 1 MAL H0A 6 0.360 1.008 30 | 11 HO 1 MAL H0B 7 0.360 1.008 31 | 32 | [ bonds ] 33 | ; ai aj funct c0(nm) c1(kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 34 | 7 1 1 0.1229 476976.0 ; 1.229 570 OD-CD 35 | 8 1 1 0.1364 376560.0 ; 1.364 450 OH-CD 36 | 2 1 1 0.1522 265265.6 ; 1.522 317 CT-CD 37 | 10 8 1 0.0945 463750.4 ; 0.945 553 HO-OH 38 | 5 2 1 0.1552 265265.6 ; 1.522 317 CD-CT 39 | 3 2 1 0.1090 284512.0 ; 1.090 340 HC-CT 40 | 4 2 1 0.1090 284512.0 ; 1.090 340 HC-CT 41 | 6 5 1 0.1229 476976.0 ; 1.229 570 OD-CD 42 | 9 5 1 0.1364 376560.0 ; 1.364 450 OH-CD 43 | 11 9 1 0.0945 462750.4 ; 0.945 553 HO-OH 44 | 45 | [ angles ] 46 | ; ai aj ak funct c0(deg) c1(kj mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 47 | 7 1 8 1 121.0 669.440 ; 121.0 80 OD-CD-OH 48 | 7 1 2 1 120.4 669.440 ; 120.4 80 OD-CD-CT 49 | 1 8 10 1 113.0 292.880 ; 113.0 35 CD-OH-HO 50 | 1 2 5 1 111.1 527.184 ; 111.1 63 CD-CT-CD 51 | 1 2 3 1 109.5 292.880 ; 109.5 35 CD-CT-HC 52 | 1 2 4 1 109.5 292.880 ; 109.5 35 CD-CT-HC 53 | 2 5 6 1 120.4 669.440 ; 120.4 80 CT-CD-OD 54 | 2 5 9 1 108.0 585.760 ; 108.0 70 CT-CD-OH 55 | 5 9 11 1 113.0 292.880 ; 113.0 35 CD-OH-HO 56 | 8 1 2 1 108.0 585.760 ; 108.0 70 OH-CD-CT 57 | 5 2 3 1 109.5 292.880 ; 109.5 35 CD-CT-HC 58 | 5 2 4 1 109.5 292.880 ; 109.5 35 CD-CT-HC 59 | 3 2 4 1 107.8 276.144 ; 107.8 33 HC-CT-HC 60 | 6 5 9 1 121.0 669.440 ; 121.0 80 OD-CD-OH 61 | 62 | [ dihedrals ] 63 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 64 | 2 1 7 8 5 0.0000 87.8640 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 CT-CD-OD-OH improper 65 | 7 1 8 10 5 0.0000 23.0120 0.0000 0.0000 ; 0.000 5.500 0.000 0.000 OD-CD-OH-HO 66 | 7 1 2 5 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OD-CD-CT-CD 67 | 3 1 2 5 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HC-CT-CD-CD improper 68 | 4 2 1 5 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HC-CT-CD-CD improper 69 | 1 2 5 6 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 CD-CT-CD-OD 70 | 9 5 6 2 5 0.0000 87.8640 0.0000 0.0000 ; 0.000 21.000 0.000 0.000 OH-CD-OD-CT improper 71 | 11 9 5 6 5 0.0000 23.0120 0.0000 0.0000 ; 0.000 5.500 0.000 0.000 HO-OH-CD-OD 72 | 10 8 1 2 5 6.2760 23.0120 0.0000 0.0000 ; 1.500 5.500 0.000 0.000 HO-OH-CD-CT 73 | 3 2 1 7 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HC-CT-CD-OD 74 | 4 2 1 7 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HC-CT-CD-OD 75 | 5 2 1 8 5 4.1840 2.2845 1.8828 0.0000 ; 1.000 0.546 0.450 0.000 CD-CT-CD-OH 76 | 3 2 1 8 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HC-CT-CD-OH 77 | 4 2 1 8 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 HC-CT-CD-OH 78 | 1 2 5 9 5 4.1840 2.2845 1.8828 0.0000 ; 1.000 0.546 0.450 0.000 CD-CT-CD-OH 79 | 6 5 2 3 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OD-CD-CT-HC 80 | 9 5 2 3 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OH-CD-CT-HC 81 | 6 5 2 4 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OD-CD-CT-HC 82 | 9 5 2 4 5 0.0000 0.0000 0.0000 0.0000 ; 0.000 0.000 0.000 0.000 OH-CD-CT-HC 83 | 11 9 5 2 5 6.2760 23.0120 0.0000 0.0000 ; 1.500 5.500 0.000 0.000 HO-OH-CD-CT 84 | 85 | [ exclusions ] 86 | 3 6 87 | 4 6 88 | 3 7 89 | 4 7 90 | 91 | -------------------------------------------------------------------------------- /DES/ITP/malonic_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Malonic Acid HBD [MAL] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma(Ang.) epsilon(kcal/mol) 16 | CD 12.011 0.416 A 0.3750 1.09830 ; 3.75 0.2625 17 | CT 12.011 -0.096 A 0.3500 0.69035 ; 3.50 0.1650 18 | HC 1.008 0.048 A 0.2500 0.31380 ; 2.50 0.0750 19 | OD 15.999 -0.352 A 0.2960 2.19660 ; 2.96 0.5250 20 | OH 15.999 -0.424 A 0.3000 1.77820 ; 3.00 0.4250 21 | HO 1.008 0.360 A 0.0000 0.00000 ; 0.00 0.0000 22 | 23 | -------------------------------------------------------------------------------- /DES/ITP/oxalic_DES.itp: -------------------------------------------------------------------------------- 1 | ; Oxalic Acid HBD [OXA] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | OXA 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 CD 1 OXA C01 1 0.416 12.011 21 | 2 CD 1 OXA C02 2 0.416 12.011 22 | 3 OH 1 OXA O03 3 -0.394 15.999 23 | 4 HO 1 OXA H04 3 0.330 1.008 24 | 5 OH 1 OXA O05 4 -0.394 15.999 25 | 6 HO 1 OXA H06 4 0.330 1.008 26 | 7 OD 1 OXA O07 5 -0.352 15.999 27 | 8 OD 1 OXA O08 6 -0.352 15.999 28 | 29 | [ bonds ] 30 | ; ai aj funct c0(nm) c1(kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 31 | 1 2 1 0.1510 292880.0 ; 1.510 350 CD-CD 32 | 7 1 1 0.1229 476976.0 ; 1.229 570 OD-CD 33 | 3 1 1 0.1364 376560.0 ; 1.364 450 OH-CD 34 | 8 2 1 0.1229 476976.0 ; 1.229 570 OD-CD 35 | 5 2 1 0.1364 376560.0 ; 1.364 450 OH-CD 36 | 4 3 1 0.0945 462750.0 ; 0.945 553 HO-OH 37 | 6 5 1 0.0945 463750.0 ; 0.945 553 HO-OH 38 | 39 | [ angles ] 40 | ; ai aj ak funct c0(deg) c1(kj mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 41 | 1 2 8 1 121.40 669.44 ; 121.40 80.00 CD-CD-OD 42 | 1 2 5 1 118.03 593.79 ; 118.03 70.96 CD-CD-OH 43 | 2 1 7 1 121.40 669.44 ; 121.40 80.00 CD-CD-OD 44 | 2 1 3 1 118.03 593.79 ; 118.03 70.96 CD-CD-OH 45 | 1 3 4 1 113.00 292.88 ; 113.00 35.00 CD-OH-HO 46 | 2 5 6 1 113.00 292.88 ; 113.00 35.00 CD-OH-HO 47 | 3 1 7 1 121.00 669.44 ; 121.00 80.00 OH-CD-OD 48 | 8 2 5 1 121.00 669.44 ; 121.00 80.00 OD-CD-OH 49 | 50 | [ dihedrals ] 51 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 52 | 5 2 8 1 5 0.0000 87.8640 0.0000 0.0000 ; 0.00 21.00 0.00 0.00 OH-CD-OD-CD improper 53 | 7 1 2 8 5 6.6944 13.3888 0.0000 0.0000 ; 1.60 3.20 0.00 0.00 OD-CD-CD-OD 54 | 3 1 7 2 5 0.0000 87.8640 0.0000 0.0000 ; 0.00 21.00 0.00 0.00 OH-CD-OD-CD improper 55 | 6 5 2 8 5 0.0000 23.0120 0.0000 0.0000 ; 0.00 5.50 0.00 0.00 HO-OH-CD-OD 56 | 4 3 1 7 5 0.0000 23.0120 0.0000 0.0000 ; 0.00 5.50 0.00 0.00 HO-OH-CD-OD 57 | 5 2 1 3 5 6.6944 13.3888 0.0000 0.0000 ; 1.60 3.20 0.00 0.00 OH-CD-CD-OH 58 | 8 2 1 3 5 6.6944 13.3888 0.0000 0.0000 ; 1.60 3.20 0.00 0.00 OD-CD-CD-OH 59 | 5 2 1 7 5 6.6944 13.3888 0.0000 0.0000 ; 1.60 3.20 0.00 0.00 OH-CD-CD-OD 60 | 4 3 1 2 5 12.5520 23.0120 0.0000 0.0000 ; 3.00 5.50 0.00 0.00 HO-OH-CD-CD 61 | 6 5 2 1 5 12.5520 12.0120 0.0000 0.0000 ; 3.00 5.50 0.00 0.00 HO-OH-CD-CD 62 | 63 | [ exclusions ] 64 | 6 8 65 | 6 7 66 | 4 8 67 | 4 7 68 | 6 3 69 | 4 5 70 | 71 | -------------------------------------------------------------------------------- /DES/ITP/oxalic_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Oxalic Acid HBD [OXA] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma(Ang.) epsilon(kcal/mol) 16 | CD 12.011 0.416 A 0.3750 0.65898 ; 3.75 0.1575 17 | OH 15.999 -0.394 A 0.2920 1.06692 ; 2.92 0.2550 18 | HO 1.008 0.330 A 0.0000 0.00000 ; 0.00 0.0000 19 | OD 15.999 -0.352 A 0.2960 1.31796 ; 2.96 0.3150 20 | 21 | -------------------------------------------------------------------------------- /DES/ITP/phenol_DES.itp: -------------------------------------------------------------------------------- 1 | ; Phenol HBD [PHE] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | 15 | [ moleculetype ] 16 | ; name nrexcl 17 | PHE 3 18 | 19 | [ atoms ] 20 | ; nr type resnr residu atom cgnr charge mass 21 | 1 CB 1 PHE CB 1 -0.092 12.011 22 | 2 CB 1 PHE CB 1 -0.092 12.011 23 | 3 CB 1 PHE CB 1 -0.092 12.011 24 | 4 CB 1 PHE CB 1 -0.092 12.011 25 | 5 CO 1 PHE CO 1 0.120 12.011 26 | 6 CB 1 PHE CB 1 -0.092 12.011 27 | 7 HB 1 PHE HB 1 0.092 1.008 28 | 8 HB 1 PHE HB 1 0.092 1.008 29 | 9 HB 1 PHE HB 1 0.092 1.008 30 | 10 HB 1 PHE HB 1 0.092 1.008 31 | 11 HB 1 PHE HB 1 0.092 1.008 32 | 12 OH 1 PHE OH 1 -0.468 15.999 33 | 13 HO 1 PHE HO 1 0.348 1.008 34 | 35 | [ bonds ] 36 | ; ai aj funct c0(nm) c1(kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 37 | 6 1 1 0.1400 392459.20 ; 1.400 469 CB-CB 38 | 1 2 1 0.1400 392459.20 ; 1.400 469 CB-CB 39 | 2 3 1 0.1400 392459.20 ; 1.400 469 CB-CB 40 | 3 4 1 0.1400 392459.20 ; 1.400 469 CB-CB 41 | 5 4 1 0.1400 392359.20 ; 1.400 469 CO-CB 42 | 5 6 1 0.1400 392359.20 ; 1.400 469 CO-CB 43 | 1 7 1 0.1080 307105.60 ; 1.080 367 HB-CB 44 | 2 8 1 0.1080 307105.60 ; 1.080 367 HB-CB 45 | 3 9 1 0.1080 307105.60 ; 1.080 367 HB-CB 46 | 4 10 1 0.1080 307105.60 ; 1.080 367 HB-CB 47 | 6 11 1 0.1080 307105.60 ; 1.080 367 HB-CB 48 | 12 5 1 0.1365 376560.00 ; 1.365 450 OH-CO 49 | 13 12 1 0.0945 462750.40 ; 0.945 553 HO-OH 50 | 51 | [ angles ] 52 | ; ai aj ak funct c0(deg) c1(kj mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 53 | 6 1 2 1 120.0 527.184 ; 120.0 63.0 CB-CB-CB 54 | 1 2 3 1 120.0 527.184 ; 120.0 63.0 CB-CB-CB 55 | 2 3 4 1 120.0 527.184 ; 120.0 63.0 CB-CB-CB 56 | 5 6 1 1 120.0 527.184 ; 120.0 63.0 CO-CB-CB 57 | 5 4 3 1 120.0 527.184 ; 120.0 63.0 CO-CB-CB 58 | 4 5 12 1 120.0 585.760 ; 120.0 70.0 CB-CO-OH 59 | 6 5 12 1 120.0 585.769 ; 120.0 70.0 CB-CO-OH 60 | 6 1 7 1 120.0 292.880 ; 120.0 35.0 CB-CB-HB 61 | 1 2 8 1 120.0 292.880 ; 120.0 35.0 CB-CB-HB 62 | 2 3 9 1 120.0 292.880 ; 120.0 35.0 CB-CB-HB 63 | 3 4 10 1 120.0 292.880 ; 120.0 35.0 CB-CB-HB 64 | 4 3 9 1 120.0 292.880 ; 120.0 35.0 CB-CB-HB 65 | 3 2 8 1 120.0 292.880 ; 120.0 35.0 CB-CB-HB 66 | 2 1 7 1 120.0 292.880 ; 120.0 35.0 CB-CB-HB 67 | 1 6 11 1 120.0 292.880 ; 120.0 35.0 CB-CB-HB 68 | 5 4 10 1 120.0 292.880 ; 120.0 35.0 CO-CB-HB 69 | 5 6 11 1 120.0 292.880 ; 120.0 35.0 CO-CB-HB 70 | 5 12 13 1 113.0 292.880 ; 113.0 35.0 CO-OH-HO 71 | 4 5 6 1 120.0 527.184 ; 120.0 63.0 CB-CO-CB 72 | 73 | [ dihedrals ] 74 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 75 | 13 12 5 4 5 0.000 7.037 0.000 0.000 ; 0.00 1.68 0.00 0.00 HO-OH-CO-CB 76 | 13 12 5 6 5 0.000 7.037 0.000 0.000 ; 0.00 1.68 0.00 0.00 HO-OH-CO-CB 77 | 6 1 2 3 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CB-CB 78 | 1 2 3 4 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CB-CB 79 | 5 6 1 2 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CO-CB-CB-CB 80 | 5 4 3 2 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CO-CB-CB-CB 81 | 3 4 5 6 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CO-CB 82 | 4 5 6 1 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CO-CB-CB 83 | 6 1 2 8 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CB-HB 84 | 1 2 3 9 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CB-HB 85 | 2 3 4 10 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CB-HB 86 | 4 3 2 8 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CB-HB 87 | 3 2 1 7 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CB-HB 88 | 2 1 6 11 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CB-CB-HB 89 | 5 4 3 9 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CO-CB-CB-HB 90 | 5 6 1 7 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CO-CB-CB-HB 91 | 4 5 6 11 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CO-CB-HB 92 | 6 5 4 10 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 CB-CO-CB-HB 93 | 12 5 4 3 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 OH-CO-CB-CB 94 | 12 5 6 1 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 OH-CO-CB-CB 95 | 12 5 4 10 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 OH-CO-CB-HB 96 | 12 5 6 11 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 OH-CO-CB-HB 97 | 11 6 1 7 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 HB-CB-CB-HB 98 | 7 1 2 8 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 HB-CB-CB-HB 99 | 8 2 3 9 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 HB-CB-CB-HB 100 | 9 3 4 10 5 0.000 30.334 0.000 0.000 ; 0.00 7.25 0.00 0.00 HB-CB-CB-HB 101 | 102 | -------------------------------------------------------------------------------- /DES/ITP/phenol_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Phenol HBD [PHE] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma(Ang.) epsilon(kcal/mol) 16 | CB 12.011 -0.092 A 0.3550 0.322168 ; 3.55 0.077 17 | CO 12.011 0.120 A 0.3550 0.322168 ; 3.55 0.077 18 | HB 1.008 0.092 A 0.2420 0.138072 ; 2.42 0.033 19 | OH 15.999 -0.468 A 0.3070 0.782408 ; 3.07 0.187 20 | HO 1.008 0.348 A 0.0000 0.000000 ; 0.00 0.000 21 | 22 | -------------------------------------------------------------------------------- /DES/ITP/urea_DES.itp: -------------------------------------------------------------------------------- 1 | ; Urea HBD [UREA] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ moleculetype ] 15 | ; name nrexcl 16 | UREA 3 17 | 18 | [ atoms ] 19 | ; nr type resnr residu atom cgnr charge mass 20 | 1 C 1 UREA C 1 0.124 12.011 21 | 2 O 1 UREA O 1 -0.322 15.999 22 | 3 N 1 UREA N 1 -0.453 14.007 23 | 4 N 1 UREA N 1 -0.453 14.007 24 | 5 HT 1 UREA HT 1 0.276 1.008 25 | 6 HC 1 UREA HC 1 0.276 1.008 26 | 7 HT 1 UREA HT 1 0.276 1.008 27 | 8 HC 1 UREA HC 1 0.276 1.008 28 | 29 | [ bonds ] 30 | ; ai aj funct c0 (nm) c1 (kj mol-1 nm-2) ro(Ang.) kr(kcal mol-1 Ang.-2) 31 | 1 2 1 0.1229 476976.000 ; 1.229 570 C-O 32 | 1 3 1 0.1335 410032.000 ; 1.335 490 C-N 33 | 1 4 1 0.1335 410032.000 ; 1.335 490 C-N 34 | 3 7 1 0.1010 363171.200 ; 1.010 434 N-HT 35 | 3 8 1 0.1010 363171.200 ; 1.010 434 N-HC 36 | 4 5 1 0.1010 363171.200 ; 1.010 434 N-HT 37 | 4 6 1 0.1010 363171.200 ; 1.010 434 N-HC 38 | 39 | [ angles ] 40 | ; ai aj ak funct c0 (deg) c1 (kJ mol-1 rad-2) c0(deg) c1(kcal mol-1 rad-2) 41 | 2 1 3 1 122.9 669.440 ; 122.9 80 O-C-N 42 | 2 1 4 1 122.9 669.440 ; 122.9 80 O-C-N 43 | 1 3 7 1 119.8 292.880 ; 119.8 35 C-N-HT 44 | 1 3 8 1 119.8 292.880 ; 119.8 35 C-N-HC 45 | 1 4 5 1 119.8 292.880 ; 119.8 35 C-N-HT 46 | 1 4 6 1 119.8 292.880 ; 119.8 35 C-N-HC 47 | 3 1 4 1 114.2 585.760 ; 114.2 70 N-C-N 48 | 5 4 6 1 120.0 292.880 ; 120.0 35 HT-N-HC 49 | 7 3 8 1 120.0 292.880 ; 120.0 35 HT-N-HC 50 | 51 | [ dihedrals ] 52 | ; ai aj ak al funct c0 c1 c2 c3 (kj/mol) V1 V2 V3 V4 (kcal/mol) 53 | 2 1 3 7 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 O-C-N-HT 54 | 2 1 3 8 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 O-C-N-HC 55 | 2 1 4 5 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 O-C-N-HT 56 | 2 1 4 6 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 O-C-N-HC 57 | 7 3 1 4 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 HT-N-C-N 58 | 8 3 1 4 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 HC-N-C-N 59 | 5 4 1 3 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 HT-N-C-N 60 | 6 4 1 3 5 0.0000 20.5016 0.0000 0.0000 ; 0.00 4.90 0.00 0.00 HC-N-C-N 61 | 7 3 1 8 5 0.0000 20.9200 0.0000 0.0000 ; 0.00 5.00 0.00 0.00 HT-N-C-HC improper 62 | 5 4 1 6 5 0.0000 20.9200 0.0000 0.0000 ; 0.00 5.00 0.00 0.00 HT-N-C-HC improper 63 | 2 1 3 4 5 0.0000 87.8640 0.0000 0.0000 ; 0.00 21.00 0.00 0.00 O-C-N-N improper 64 | 65 | -------------------------------------------------------------------------------- /DES/ITP/urea_atomtypes_DES.itp: -------------------------------------------------------------------------------- 1 | ; Urea HBD [UREA] 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | [ atomtypes ] 15 | ; type mass charge ptype sigma (nm) epsilon (kj/mol) sigma(Ang.) epsilon(kcal/mol) 16 | C 12.011 0.124 A 0.375 0.65898 ; 3.75 0.1575 17 | O 15.999 -0.322 A 0.296 1.31796 ; 2.96 0.3150 18 | N 14.007 -0.453 A 0.355 1.06692 ; 3.55 0.2550 19 | HT 1.008 0.276 A 0.000 0.00000 ; 0.00 0.0000 20 | HC 1.008 0.276 A 0.000 0.00000 ; 0.00 0.0000 21 | -------------------------------------------------------------------------------- /DES/PDBs/2,2,2-trifluoroacetamide.pdb: -------------------------------------------------------------------------------- 1 | TITLE 2,2,2-trifluoroacetamide 2 | REMARK 3 | REMARK Deep Eutectic Solvent OPLS-DES force field 4 | REMARK Version 4/2021 5 | REMARK Orlando Acevedo 6 | REMARK Email: orlando.acevedo@miami.edu 7 | REMARK Contributors: X. Zhong 8 | REMARK 9 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 10 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 12 | REMARK doi: 10.1021/acs.jctc.1c00047. 13 | REMARK 14 | REMARK GROMACS 5.0.7 is recommended for the values given below 15 | HETATM 1 N00 HBD 1 1.000 1.000 0.000 16 | HETATM 2 C01 HBD 1 -0.379 1.000 0.000 17 | HETATM 3 O02 HBD 1 -0.973 1.000 1.078 18 | HETATM 4 C03 HBD 1 -1.065 0.998 -1.385 19 | HETATM 5 F04 HBD 1 -0.152 0.997 -2.402 20 | HETATM 6 F05 HBD 1 -1.849 -0.097 -1.577 21 | HETATM 7 F06 HBD 1 -1.850 2.092 -1.581 22 | HETATM 8 H07 HBD 1 1.480 1.000 0.891 23 | HETATM 9 H08 HBD 1 1.539 1.001 -0.859 24 | END 25 | -------------------------------------------------------------------------------- /DES/PDBs/N,N-diethylethanolammonium.pdb: -------------------------------------------------------------------------------- 1 | TITLE N,N-diethylethanolammonium 2 | REMARK 3 | REMARK Deep Eutectic Solvent OPLS-DES force field 4 | REMARK Version 4/2021 5 | REMARK Orlando Acevedo 6 | REMARK Email: orlando.acevedo@miami.edu 7 | REMARK Contributors: X. Zhong 8 | REMARK 9 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 10 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 12 | REMARK doi: 10.1021/acs.jctc.1c00047. 13 | REMARK 14 | REMARK GROMACS 5.0.7 is recommended for the values given below 15 | HETATM 1 C00 MOL 1 1.000 1.000 0.000 16 | HETATM 2 C01 MOL 1 -0.517 1.000 0.000 17 | HETATM 3 N02 MOL 1 -1.086 1.000 1.405 18 | HETATM 4 H03 MOL 1 -0.810 0.084 1.801 19 | HETATM 5 C04 MOL 1 -0.561 2.062 2.342 20 | HETATM 6 C05 MOL 1 -1.006 3.454 1.933 21 | HETATM 7 C06 MOL 1 -2.613 0.898 1.427 22 | HETATM 8 C07 MOL 1 -3.043 -0.467 0.877 23 | HETATM 9 O08 MOL 1 -2.133 -1.447 1.381 24 | HETATM 10 H09 MOL 1 1.367 0.774 -1.007 25 | HETATM 11 H0A MOL 1 1.404 0.247 0.683 26 | HETATM 12 H0B MOL 1 1.400 1.981 0.276 27 | HETATM 13 H0C MOL 1 -0.860 0.084 -0.488 28 | HETATM 14 H0D MOL 1 -0.927 1.862 -0.537 29 | HETATM 15 H0E MOL 1 0.530 1.980 2.361 30 | HETATM 16 H0F MOL 1 -0.924 1.815 3.345 31 | HETATM 17 H0G MOL 1 -0.823 3.658 0.875 32 | HETATM 18 H0H MOL 1 -0.461 4.204 2.515 33 | HETATM 19 H0I MOL 1 -2.073 3.599 2.132 34 | HETATM 20 H0J MOL 1 -3.034 1.735 0.858 35 | HETATM 21 H0K MOL 1 -2.907 0.974 2.483 36 | HETATM 22 H0M MOL 1 -2.996 -0.480 -0.216 37 | HETATM 23 H0N MOL 1 -4.063 -0.707 1.188 38 | HETATM 24 H0O MOL 1 -2.420 -2.312 1.020 39 | END 40 | -------------------------------------------------------------------------------- /DES/PDBs/N-ethyl-N,N-dimethylethanolammonium.pdb: -------------------------------------------------------------------------------- 1 | TITLE N-ethyl-N,N-dimethylethanolammonium 2 | REMARK 3 | REMARK Deep Eutectic Solvent OPLS-DES force field 4 | REMARK Version 4/2021 5 | REMARK Orlando Acevedo 6 | REMARK Email: orlando.acevedo@miami.edu 7 | REMARK Contributors: X. Zhong 8 | REMARK 9 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 10 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 12 | REMARK doi: 10.1021/acs.jctc.1c00047. 13 | REMARK 14 | REMARK GROMACS 5.0.7 is recommended for the values given below 15 | HETATM 1 C00 MOL 1 1.000 1.000 0.000 16 | HETATM 2 C01 MOL 1 -0.521 1.000 0.000 17 | HETATM 3 N02 MOL 1 -1.167 1.000 1.403 18 | HETATM 4 C03 MOL 1 -0.733 -0.235 2.195 19 | HETATM 5 C04 MOL 1 -0.780 2.251 2.181 20 | HETATM 6 C05 MOL 1 -2.713 0.974 1.153 21 | HETATM 7 C06 MOL 1 -3.593 0.967 2.412 22 | HETATM 8 O07 MOL 1 -3.407 -0.232 3.153 23 | HETATM 9 H08 MOL 1 1.357 1.001 -1.035 24 | HETATM 10 H09 MOL 1 1.416 0.106 0.474 25 | HETATM 11 H0A MOL 1 1.415 1.885 0.483 26 | HETATM 12 H0B MOL 1 -0.891 0.109 -0.523 27 | HETATM 13 H0C MOL 1 -0.891 1.891 -0.521 28 | HETATM 14 H0D MOL 1 0.357 -0.250 2.253 29 | HETATM 15 H0E MOL 1 -1.107 -1.126 1.682 30 | HETATM 16 H0F MOL 1 -1.112 -0.161 3.216 31 | HETATM 17 H0G MOL 1 0.302 2.253 2.332 32 | HETATM 18 H0H MOL 1 -1.271 2.230 3.157 33 | HETATM 19 H0I MOL 1 -1.092 3.127 1.606 34 | HETATM 20 H0J MOL 1 -2.905 0.065 0.569 35 | HETATM 21 H0K MOL 1 -2.944 1.853 0.541 36 | HETATM 22 H0M MOL 1 -4.647 1.026 2.118 37 | HETATM 23 H0N MOL 1 -3.391 1.824 3.060 38 | HETATM 24 H0O MOL 1 -4.219 -0.767 3.090 39 | END 40 | -------------------------------------------------------------------------------- /DES/PDBs/acetamide.pdb: -------------------------------------------------------------------------------- 1 | TITLE acetamide 2 | REMARK 3 | REMARK Deep Eutectic Solvent OPLS-DES force field 4 | REMARK Version 4/2021 5 | REMARK Orlando Acevedo 6 | REMARK Email: orlando.acevedo@miami.edu 7 | REMARK Contributors: X. Zhong 8 | REMARK 9 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 10 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 12 | REMARK doi: 10.1021/acs.jctc.1c00047. 13 | REMARK 14 | REMARK GROMACS 5.0.7 is recommended for the values given below 15 | HETATM 1 C00 HBD 1 1.000 1.000 0.000 16 | HETATM 2 C01 HBD 1 -0.502 1.000 0.000 17 | HETATM 3 N02 HBD 1 -1.088 1.000 1.229 18 | HETATM 4 O03 HBD 1 -1.172 1.001 -1.025 19 | HETATM 5 H04 HBD 1 1.402 1.000 1.017 20 | HETATM 6 H05 HBD 1 1.357 1.895 -0.516 21 | HETATM 7 H06 HBD 1 1.357 0.105 -0.516 22 | HETATM 8 H07 HBD 1 -0.568 1.000 2.094 23 | HETATM 9 H08 HBD 1 -2.099 1.001 1.265 24 | END 25 | -------------------------------------------------------------------------------- /DES/PDBs/chloride.pdb: -------------------------------------------------------------------------------- 1 | TITLE Chloride anion [cl] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 Cl 0 -0.381 0.502 0.000 Cl 11 | END 12 | -------------------------------------------------------------------------------- /DES/PDBs/choline.pdb: -------------------------------------------------------------------------------- 1 | TITLE Choline cation [Chol] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 CS 0 0.362 0.576 0.000 C 11 | HETATM 2 HS 0 0.719 1.081 0.874 H 12 | HETATM 3 HS 0 0.719 1.081 -0.874 H 13 | HETATM 4 NA 0 -1.108 0.576 0.000 N 14 | HETATM 5 CW 0 0.876 -0.876 0.000 C 15 | HETATM 6 HW 0 0.519 -1.380 -0.874 H 16 | HETATM 7 HW 0 0.519 -1.380 0.874 H 17 | HETATM 8 OY 0 2.306 -0.876 0.000 O 18 | HETATM 9 HY 0 2.626 -1.781 0.000 H 19 | HETATM 10 CA 0 -1.598 -0.117 1.200 C 20 | HETATM 11 HA 0 -2.581 0.232 1.437 H 21 | HETATM 12 HA 0 -1.627 -1.170 1.017 H 22 | HETATM 13 HA 0 -0.941 0.084 2.021 H 23 | HETATM 14 CA 0 -1.598 1.962 0.000 C 24 | HETATM 15 HA 0 -1.270 2.456 0.891 H 25 | HETATM 16 HA 0 -1.212 2.477 -0.855 H 26 | HETATM 17 HA 0 -2.667 1.962 -0.036 H 27 | HETATM 18 CA 0 -1.598 -0.117 -1.200 C 28 | HETATM 19 HA 0 -2.626 0.131 -1.360 H 29 | HETATM 20 HA 0 -1.021 0.188 -2.049 H 30 | HETATM 21 HA 0 -1.502 -1.174 -1.066 H 31 | END 32 | -------------------------------------------------------------------------------- /DES/PDBs/ethylammonium.pdb: -------------------------------------------------------------------------------- 1 | TITLE ethylammonium 2 | REMARK 3 | REMARK Deep Eutectic Solvent OPLS-DES force field 4 | REMARK Version 4/2021 5 | REMARK Orlando Acevedo 6 | REMARK Email: orlando.acevedo@miami.edu 7 | REMARK Contributors: X. Zhong 8 | REMARK 9 | REMARK Zhong, X.; Velez, C.; Acevedo, O. 10 | REMARK Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | REMARK J. Chem. Theory Comput. 2021, 17, (in press). 12 | REMARK doi: 10.1021/acs.jctc.1c00047. 13 | REMARK 14 | REMARK GROMACS 5.0.7 is recommended for the values given below 15 | HETATM 1 C00 MOL 1 1.000 1.000 0.000 16 | HETATM 2 C01 MOL 1 -0.513 1.000 0.000 17 | HETATM 3 N02 MOL 1 -0.999 1.000 1.399 18 | HETATM 4 H03 MOL 1 -0.675 0.170 1.913 19 | HETATM 5 H04 MOL 1 -0.675 1.830 1.913 20 | HETATM 6 H05 MOL 1 -2.027 0.999 1.433 21 | HETATM 7 H06 MOL 1 1.377 0.999 -1.028 22 | HETATM 8 H07 MOL 1 1.395 0.113 0.507 23 | HETATM 9 H08 MOL 1 1.395 1.888 0.505 24 | HETATM 10 H09 MOL 1 -0.917 0.105 -0.481 25 | HETATM 11 H0A MOL 1 -0.917 1.895 -0.481 26 | END 27 | -------------------------------------------------------------------------------- /DES/PDBs/ethylene_glycol.pdb: -------------------------------------------------------------------------------- 1 | TITLE Ethylene Glycol HBD [ETGLY] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 C01 0 -1.539 0.438 0.003 C 11 | HETATM 2 H02 0 -0.705 0.199 0.629 H 12 | HETATM 3 H03 0 -2.035 -0.464 -0.289 H 13 | HETATM 4 C04 0 -1.042 1.179 -1.253 C 14 | HETATM 5 H05 0 -1.876 1.417 -1.879 H 15 | HETATM 6 H06 0 -0.545 2.080 -0.961 H 16 | HETATM 7 O07 0 -0.130 0.343 -1.970 O 17 | HETATM 8 H08 0 0.179 0.805 -2.753 H 18 | HETATM 9 O09 0 -2.450 1.274 0.720 O 19 | HETATM 10 H10 0 -2.760 0.812 1.503 H 20 | END 21 | -------------------------------------------------------------------------------- /DES/PDBs/glycerol.pdb: -------------------------------------------------------------------------------- 1 | TITLE Glycerol HBD [GLY] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 CM 0 0.023 0.048 -0.223 C 11 | HETATM 2 OM 0 -0.076 1.361 0.313 O 12 | HETATM 3 CB 0 -1.205 -0.751 0.176 C 13 | HETATM 4 CB 0 1.296 -0.574 0.305 C 14 | HETATM 5 HM 0 -0.970 1.663 0.067 H 15 | HETATM 6 HZ 0 0.081 0.077 -1.322 H 16 | HETATM 7 HC 0 -1.237 -0.841 1.270 H 17 | HETATM 8 HC 0 -1.181 -1.756 -0.266 H 18 | HETATM 9 HC 0 1.275 -1.662 0.137 H 19 | HETATM 10 HC 0 1.340 -0.389 1.386 H 20 | HETATM 11 OH 0 -2.323 0.001 -0.311 O 21 | HETATM 12 OH 0 2.390 0.027 -0.381 O 22 | HETATM 13 HO 0 -3.128 -0.350 0.102 H 23 | HETATM 14 HO 0 3.200 -0.191 0.109 H 24 | END 25 | -------------------------------------------------------------------------------- /DES/PDBs/levulinic.pdb: -------------------------------------------------------------------------------- 1 | TITLE Levulinic Acid HBD [LEV] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 C0A 0 -1.956 0.165 -0.000 C 11 | HETATM 2 O0B 0 -3.027 -0.682 -0.000 O 12 | HETATM 3 H0C 0 -2.712 -1.604 -0.000 H 13 | HETATM 4 O0D 0 -2.132 1.366 -0.000 O 14 | HETATM 5 C0E 0 -0.600 -0.510 0.001 C 15 | HETATM 6 H0F 0 -0.524 -1.168 0.874 H 16 | HETATM 7 H0G 0 -0.523 -1.169 -0.872 H 17 | HETATM 8 C0H 0 0.536 0.498 0.001 C 18 | HETATM 9 H0I 0 0.460 1.163 -0.868 H 19 | HETATM 10 H0J 0 0.460 1.162 0.871 H 20 | HETATM 11 C0K 0 1.896 -0.170 -0.000 C 21 | HETATM 12 C0L 0 3.100 0.744 -0.000 C 22 | HETATM 13 H0M 0 4.011 0.146 -0.001 H 23 | HETATM 14 H0N 0 3.082 1.393 -0.882 H 24 | HETATM 15 H0O 0 3.083 1.393 0.881 H 25 | HETATM 16 O0P 0 2.010 -1.394 -0.000 O 26 | END 27 | -------------------------------------------------------------------------------- /DES/PDBs/malonic.pdb: -------------------------------------------------------------------------------- 1 | TITLE Malonic Acid HBD [MAL] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 C01 0 -0.078 0.013 1.257 C 11 | HETATM 2 C02 0 -0.790 -0.519 0.000 C 12 | HETATM 3 H03 0 -0.762 -1.589 0.000 H 13 | HETATM 4 H04 0 -1.808 -0.189 0.000 H 14 | HETATM 5 C05 0 -0.078 0.013 -1.257 C 15 | HETATM 6 O06 0 0.504 1.128 -1.226 O 16 | HETATM 7 O07 0 0.504 1.128 1.226 O 17 | HETATM 8 O08 0 -0.078 -0.760 2.460 O 18 | HETATM 9 O09 0 -0.078 -0.760 -2.460 O 19 | HETATM 10 H0A 0 0.723 -0.579 2.957 H 20 | HETATM 11 H0B 0 0.723 -0.579 -2.957 H 21 | END 22 | -------------------------------------------------------------------------------- /DES/PDBs/oxalic_acid.pdb: -------------------------------------------------------------------------------- 1 | TITLE Oxalic Acid HBD [OXA] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 C01 0 -0.371 0.675 -0.000 C 11 | HETATM 2 C02 0 0.371 -0.675 -0.000 C 12 | HETATM 3 O03 0 0.371 1.898 0.000 O 13 | HETATM 4 H04 0 -0.237 2.641 0.000 H 14 | HETATM 5 O05 0 -0.371 -1.898 0.000 O 15 | HETATM 6 H06 0 0.237 -2.641 0.000 H 16 | HETATM 7 O07 0 -1.629 0.702 -0.000 O 17 | HETATM 8 O08 0 1.629 -0.702 -0.000 O 18 | END 19 | -------------------------------------------------------------------------------- /DES/PDBs/phenol.pdb: -------------------------------------------------------------------------------- 1 | TITLE Phenol HBD [PHE] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 CB 0 1.423 1.526 0.858 C 11 | HETATM 2 CB 0 1.030 0.489 0.001 C 12 | HETATM 3 CB 0 -0.063 0.666 -0.858 C 13 | HETATM 4 CB 0 -0.764 1.880 -0.859 C 14 | HETATM 5 CO 0 -0.371 2.917 -0.002 C 15 | HETATM 6 CB 0 0.722 2.739 0.857 C 16 | HETATM 7 HB 0 2.258 1.390 1.514 H 17 | HETATM 8 HB 0 1.565 -0.438 0.002 H 18 | HETATM 9 HB 0 -0.363 -0.125 -1.513 H 19 | HETATM 10 HB 0 -1.598 2.015 -1.515 H 20 | HETATM 11 HB 0 1.022 3.531 1.512 H 21 | HETATM 12 OH 0 -1.086 4.155 -0.003 O 22 | HETATM 13 HO 0 -0.692 4.753 0.637 H 23 | END 24 | -------------------------------------------------------------------------------- /DES/PDBs/urea.pdb: -------------------------------------------------------------------------------- 1 | TITLE Urea HBD [UREA] 2 | REMARK Deep Eutectic Solvent OPLS-DES force field 3 | REMARK Version 6/2018 4 | REMARK Orlando Acevedo 5 | REMARK Email: orlando.acevedo@miami.edu 6 | REMARK Contributors: B. Doherty 7 | REMARK B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 8 | REMARK J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 9 | 10 | HETATM 1 C 2 2 0.000 0.000 1.400 C 11 | HETATM 2 O 2 2 0.000 0.000 0.000 O 12 | HETATM 3 N 2 2 -1.256 0.000 2.125 N 13 | HETATM 4 N 2 2 1.256 0.000 2.125 N 14 | HETATM 5 HT 2 2 1.072 0.000 3.116 H 15 | HETATM 6 HC 2 2 2.252 0.000 1.968 H 16 | HETATM 7 HT 2 2 -1.072 0.000 3.116 H 17 | HETATM 8 HC 2 2 -2.252 0.000 1.968 H 18 | END 19 | -------------------------------------------------------------------------------- /DES/TOP/CCEtg_DES.top: -------------------------------------------------------------------------------- 1 | ; Choline Chloride Ethylene Glycol Topology 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | 15 | #define _FF_OPLS 16 | #define _FF_OPLSAA 17 | 18 | [defaults] 19 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 20 | 1 3 yes 0.5 0.5 21 | 22 | ;;;LOAD ATOM TYPES 23 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_atomtypes_DES.itp" 24 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_atomtypes_DES.itp" 25 | #include "/HOME_DIRECTORY_PATH/Ethglyc_itp/ethgly_atomtypes_DES.itp" 26 | 27 | ;;;LOAD MOLECULES *.itp 28 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_DES.itp" 29 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_DES.itp" 30 | #include "/HOME_DIRECTORY_PATH/Ethglyc_itp/ethgly_DES.itp" 31 | 32 | [system] 33 | ; Name 34 | Neat CHOL Cl ETGLY 35 | 36 | [molecules] 37 | CHOL 500 38 | Cl 500 39 | ETGLY 1000 40 | -------------------------------------------------------------------------------- /DES/TOP/CCGly_DES.top: -------------------------------------------------------------------------------- 1 | ; Choline Chloride Glycerol Topology 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | #define _FF_OPLS 15 | #define _FF_OPLSAA 16 | 17 | [defaults] 18 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 19 | 1 3 yes 0.5 0.5 20 | 21 | ;;;LOAD ATOM TYPES 22 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_atomtypes_DES.itp" 23 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_atomtypes_DES.itp" 24 | #include "/HOME_DIRECTORY_PATH/Glycerol_itp/glycerol_atomtypes_DES.itp" 25 | 26 | ;;;LOAD MOLECULES *.itp 27 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_DES.itp" 28 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_DES.itp" 29 | #include "/HOME_DIRECTORY_PATH/Glycerol_itp/glycerol_DES.itp" 30 | 31 | [system] 32 | ; Name 33 | Neat CHOL Cl GLY 34 | 35 | [molecules] 36 | CHOL 500 37 | Cl 500 38 | GLY 1000 39 | -------------------------------------------------------------------------------- /DES/TOP/CCLev_DES.top: -------------------------------------------------------------------------------- 1 | ; Choline Chloride Levulinic Acid Topology 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | #define _FF_OPLS 15 | #define _FF_OPLSAA 16 | 17 | [defaults] 18 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 19 | 1 3 yes 0.5 0.5 20 | 21 | ;;;LOAD ATOM TYPES 22 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_atomtypes_DES.itp" 23 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_atomtypes_DES.itp" 24 | #include "/HOME_DIRECTORY_PATH/Lev_itp/levulinic_atomtypes_DES.itp" 25 | 26 | ;;;LOAD MOLECULES *.itp 27 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_DES.itp" 28 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_DES.itp" 29 | #include "/HOME_DIRECTORY_PATH/Lev_itp/levulinic_DES.itp" 30 | 31 | [system] 32 | ; Name 33 | Neat CHOL Cl lev 34 | 35 | [molecules] 36 | CHOL 500 37 | Cl 500 38 | lev 1000 39 | -------------------------------------------------------------------------------- /DES/TOP/CCMal_DES.top: -------------------------------------------------------------------------------- 1 | ; Choline Chloride Malonic Acid Topology 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | #define _FF_OPLS 15 | #define _FF_OPLSAA 16 | 17 | [defaults] 18 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 19 | 1 3 yes 0.5 0.5 20 | 21 | ;;;LOAD ATOM TYPES 22 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_atomtypes_DES.itp" 23 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_atomtypes_DES.itp" 24 | #include "/HOME_DIRECTORY_PATH/Malonic_itp/malonic_atomtypes_DES.itp" 25 | 26 | ;;;LOAD MOLECULES *.itp 27 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_DES.itp" 28 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_DES.itp" 29 | #include "/HOME_DIRECTORY_PATH/Malonic_itp/malonic_DES.itp" 30 | 31 | [system] 32 | ; Name 33 | Neat CHOL Cl MAL 34 | 35 | [molecules] 36 | CHOL 500 37 | Cl 500 38 | MAL 500 39 | -------------------------------------------------------------------------------- /DES/TOP/CCOx_DES.top: -------------------------------------------------------------------------------- 1 | ; Choline Chloride Oxalic Acid Topology 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | #define _FF_OPLS 15 | #define _FF_OPLSAA 16 | 17 | [defaults] 18 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 19 | 1 3 yes 0.5 0.5 20 | 21 | ;;;LOAD ATOM TYPES 22 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_atomtypes_DES.itp" 23 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_atomtypes_DES.itp" 24 | #include "/HOME_DIRECTORY_PATH/Oxalic_itp/oxalic_atomtypes_DES.itp" 25 | 26 | ;;;LOAD MOLECULES *.itp 27 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_DES.itp" 28 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_DES.itp" 29 | #include "/HOME_DIRECTORY_PATH/Oxalic_itp/oxalic_DES.itp" 30 | 31 | [system] 32 | ; Name 33 | Neat CHOL Cl OXA 34 | 35 | [molecules] 36 | CHOL 500 37 | Cl 500 38 | OXA 500 39 | -------------------------------------------------------------------------------- /DES/TOP/CCPhe_2.1_DES.top: -------------------------------------------------------------------------------- 1 | ; Choline Chloride Phenol (2:1) Topology 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | #define _FF_OPLS 15 | #define _FF_OPLSAA 16 | 17 | [defaults] 18 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 19 | 1 3 yes 0.5 0.5 20 | 21 | ;;;LOAD ATOM TYPES 22 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_atomtypes_DES.itp" 23 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_atomtypes_DES.itp" 24 | #include "/HOME_DIRECTORY_PATH/Phenol_itp/phenol_atomtypes_DES.itp" 25 | 26 | ;;;LOAD MOLECULES *.itp 27 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_DES.itp" 28 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_DES.itp" 29 | #include "/HOME_DIRECTORY_PATH/Phenol_itp/phenol_DES.itp" 30 | 31 | [system] 32 | ; Name 33 | Neat CHOL Cl PHE 34 | 35 | [molecules] 36 | CHOL 500 37 | Cl 500 38 | PHE 1000 39 | -------------------------------------------------------------------------------- /DES/TOP/CCPhe_3.1_DES.top: -------------------------------------------------------------------------------- 1 | ; Choline Chloride Phenol (3:1) Topology 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | #define _FF_OPLS 15 | #define _FF_OPLSAA 16 | 17 | [defaults] 18 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 19 | 1 3 yes 0.5 0.5 20 | 21 | ;;;LOAD ATOM TYPES 22 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_atomtypes_DES.itp" 23 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_atomtypes_DES.itp" 24 | #include "/HOME_DIRECTORY_PATH/Phenol_itp/phenol_atomtypes_DES.itp" 25 | 26 | ;;;LOAD MOLECULES *.itp 27 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_DES.itp" 28 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_DES.itp" 29 | #include "/HOME_DIRECTORY_PATH/Phenol_itp/phenol_DES.itp" 30 | 31 | [system] 32 | ; Name 33 | Neat CHOL Cl PHE 34 | 35 | [molecules] 36 | CHOL 500 37 | Cl 500 38 | PHE 1500 39 | -------------------------------------------------------------------------------- /DES/TOP/CCU_DES.top: -------------------------------------------------------------------------------- 1 | ; Choline Chloride Urea Topology 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 6/2018 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: B. Doherty 8 | ; 9 | ; B.Doherty, O. Acevedo, OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents 10 | ; J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647 11 | ; 12 | ; Values given below for use in GROMACS 5.0.7 and in comments are traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees) 13 | 14 | #define _FF_OPLS 15 | #define _FF_OPLSAA 16 | 17 | [defaults] 18 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 19 | 1 3 yes 0.5 0.5 20 | 21 | ;;;LOAD ATOM TYPES 22 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_atomtypes_DES.itp" 23 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_atomtypes_DES.itp" 24 | #include "/HOME_DIRECTORY_PATH/Urea_itp/urea_atomtypes_DES.itp" 25 | 26 | ;;;LOAD MOLECULES *.itp 27 | #include "/HOME_DIRECTORY_PATH/Choline_itp/choline_DES.itp" 28 | #include "/HOME_DIRECTORY_PATH/Cl_itp/cl_DES.itp" 29 | #include "/HOME_DIRECTORY_PATH/Urea_itp/urea_DES.itp" 30 | 31 | [system] 32 | ; Name 33 | Neat CHOL Cl UREA 34 | 35 | [molecules] 36 | CHOL 500 37 | Cl 500 38 | UREA 1000 39 | -------------------------------------------------------------------------------- /DES/TOP/template.top: -------------------------------------------------------------------------------- 1 | ; Template for different DES topology file 2 | ; 3 | ; Deep Eutectic Solvent OPLS-DES force field 4 | ; Version 4/2021 5 | ; Orlando Acevedo 6 | ; Email: orlando.acevedo@miami.edu 7 | ; Contributors: X. Zhong 8 | ; 9 | ; Zhong, X.; Velez, C.; Acevedo, O. 10 | ; Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations. 11 | ; J. Chem. Theory Comput. 2021, 17, (in press). 12 | ; doi: 10.1021/acs.jctc.1c00047. 13 | ; 14 | ; GROMACS 5.0.7 is recommended for the values given below 15 | 16 | #define _FF_OPLS 17 | #define _FF_OPLSAA 18 | 19 | [defaults] 20 | ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 21 | 1 3 yes 0.5 0.5 22 | 23 | ;;;LOAD ATOM TYPES 24 | #include "/HOME_DIRECTORY_PATH/ITP/salt_atomtypes_DES.itp" 25 | #include "/HOME_DIRECTORY_PATH/ITP/cl_atomtypes_DES.itp" 26 | #include "/HOME_DIRECTORY_PATH/ITP/HBD_atomtypes_DES.itp" 27 | 28 | ;;;LOAD MOLECULES 29 | #include "/HOME_DIRECTORY_PATH/ITP/salt_DES.itp" 30 | #include "/HOME_DIRECTORY_PATH/ITP/cl_DES.itp" 31 | #include "/HOME_DIRECTORY_PATH/ITP/HBD_DES.itp" 32 | 33 | [system] 34 | ; Name 35 | Neat DES 36 | 37 | [molecules] 38 | MOL 500 39 | Cl 500 40 | HBD 1000 41 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Deep eutectic solvent force field parameters (OPLS-DES) 2 | ================================================= 3 | 4 | [Orlando Acevedo](http://www.acevedoresearch.com), University of Miami 5 | 6 | This repository holds a set of OPLS-AA parameters for use in deep eutectic solvent simulations. 7 | 8 | **OPLS-AA force field parameters (OPLS-DES).** 9 | Please see the following references for technical details: 10 | 1. [doi:10.1021/acs.jpcb.8b06647](http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b06647) 11 | 2. [doi:10.1021/acs.jctc.1c00047](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.1c00047) 12 | 13 | **IMPORTANT**: Hydrogen bond donor (HBD) parameters should NOT be used for pure organic liquid simulations! HBD parameters were specifically parameterized to work exclusively with the provided ion pairs in a DES environment. 14 | 15 | Requirements 16 | ------------ 17 | * [Gromacs 5.0.7](http://www.gromacs.org/Downloads) 18 | * Tested with CUDA 7.5/8.0 and on CentOS 6.5/7.0 19 | * Heat capacity DoS calculations (g_dos) requires Gromacs 5.1.4 due to a known bug in version 5.0.7 20 | 21 | Download 22 | ----- 23 | ``` 24 | git clone git://github.com/orlandoacevedo/DES.git 25 | ``` 26 | 27 | Parameters Available 28 | -------------------- 29 | * **Ions** 30 | * choline 31 | * chloride 32 | * ethylammonium 33 | * N,N-diethylethanolammonium 34 | * N-ethyl-N,N-dimethylethanolammonium 35 | * **Hydrogen bond donors** 36 | * urea 37 | * glycerol 38 | * phenol 39 | * ethylene glycol 40 | * levulinic acid 41 | * oxalic acid 42 | * malonic acid 43 | * acetamide 44 | * 2,2,2-trifluoroacetamide 45 | 46 | * **DES** - OPLS-DES bonded and nonbonded parameters 47 | * itp, top, and pdb folders 48 | 49 | Tutorial 50 | -------- 51 | A brief tutorial is provided in the CCU-Tutorial directory. A README file will guide the user through the contruction of a CCU (reline) box using the OPLS-DES parameter set and a subsequent MD simulation. GROMACS input and output files are provided. The user is guided on how to compute the density of the deep eutetic solvent system. 52 | 53 | References 54 | ---------- 55 | Doherty, B.; Acevedo, O. "OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents" *J. Phys. Chem. B*, **2018**, *122*, 9982-9993. [doi:10.1021/acs.jpcb.8b06647](http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b06647) 56 | * Featured on the journal cover [Nov. 1, 2018 issue](https://pubs.acs.org/toc/jpcbfk/122/43) 57 | 58 | Zhong, X.; Velez, C.; Acevedo, O. "Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations" *J. Chem. Theory Comput.*, **2021**, *17*, 3078–3087. [doi:10.1021/acs.jctc.1c00047](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.1c00047) 59 | 60 | Velez, C.; Acevedo, O. "Simulation of Deep Eutectic Solvents: Progress to Promises" *WIREs Comput. Mol. Sci.*, **2022**, *12*, e1598. [doi:10.1002/wcms.1598](https://doi.org/10.1002/wcms.1598) 61 | 62 | Rukmani, S.J.; Doherty, B.; Acevedo, O.; Colina, C.M. "Molecular simulations of deep eutetic solvents: A perspective on structure, dynamics, and physical properties" *Rev. Comput. Chem.*, **2022**, *32*, 135-216. [doi:doi.org/10.1002/9781119625933.ch4](https://doi.org/10.1002/9781119625933.ch4) 63 | 64 | About 65 | ----- 66 | **Contributing Authors**: Brian Doherty, Caroline Velez, Xiang Zhong, and Orlando Acevedo* 67 | 68 | **Funding**: Gratitude is expressed to the National Science Foundation (NSF CHE-1562205 and CHE-2102038) for funding the project. 69 | 70 | **Software License**: 71 | OPLS-DES. 72 | Copyright (C) 2021 Orlando Acevedo 73 | 74 | This program is free software: you can redistribute it and/or modify 75 | it under the terms of the GNU General Public License as published by 76 | the Free Software Foundation, either version 3 of the License, or 77 | (at your option) any later version. 78 | 79 | This program is distributed in the hope that it will be useful, 80 | but WITHOUT ANY WARRANTY; without even the implied warranty of 81 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 82 | GNU General Public License for more details. 83 | --------------------------------------------------------------------------------