├── NAMD_Colvars ├── ABF │ ├── Distance.in │ ├── abf.conf │ ├── deca-ala.pdb │ ├── deca-ala.psf │ └── par_all22_prot.inp ├── WTM-eABF │ ├── Distance.in │ ├── abf.conf │ ├── deca-ala.pdb │ ├── deca-ala.psf │ └── par_all22_prot.inp ├── eABF │ ├── Distance.in │ ├── abf.conf │ ├── deca-ala.pdb │ ├── deca-ala.psf │ └── par_all22_prot.inp └── meta-eABF │ ├── Distance.in │ ├── abf.conf │ ├── deca-ala.pdb │ ├── deca-ala.psf │ └── par_all22_prot.inp ├── Openmm_Plumed ├── WTM-eABF │ ├── OpenMM_conf.py │ ├── abf.py │ ├── colvars.py │ ├── deca-ala.pdb │ ├── deca-ala.psf │ ├── par_all22_prot.inp │ └── top_all22_prot.inp ├── eABF │ ├── abf.py │ ├── colvars.py │ ├── deca-ala.pdb │ ├── deca-ala.psf │ ├── par_all22_prot.inp │ └── top_all22_prot.inp └── meta-eABF │ ├── abf.py │ ├── colvars.py │ ├── deca-ala.pdb │ ├── deca-ala.psf │ ├── par_all22_prot.inp │ └── top_all22_prot.inp └── README.md /NAMD_Colvars/ABF/Distance.in: -------------------------------------------------------------------------------- 1 | colvarsTrajFrequency 1000 2 | colvarsRestartFrequency 50000 3 | 4 | colvar { 5 | name AtomDistance 6 | 7 | width 0.1 8 | 9 | lowerboundary 12.0 10 | upperboundary 32.0 11 | 12 | lowerwallconstant 10.0 13 | upperwallconstant 10.0 14 | 15 | distance { 16 | group1 { 17 | atomnumbers { 10 } 18 | } 19 | group2 { 20 | atomnumbers { 92 } 21 | } 22 | } 23 | } 24 | 25 | 26 | abf { 27 | colvars AtomDistance 28 | fullSamples 500 29 | } 30 | -------------------------------------------------------------------------------- /NAMD_Colvars/ABF/abf.conf: -------------------------------------------------------------------------------- 1 | ################################################## 2 | ################################################## 3 | # 4 | # ABF calculation 5 | # 6 | # Deca-alanine 7 | # 8 | ################################################## 9 | ################################################## 10 | 11 | 12 | ################################################## 13 | # MD SECTION 14 | ################################################## 15 | 16 | 17 | # NUMBER OF MD-STEPS 18 | 19 | numsteps 20000000 20 | 21 | 22 | # TOPOLOGY 23 | 24 | structure deca-ala.psf 25 | 26 | 27 | # FORCE FIELD 28 | 29 | parameters par_all22_prot.inp 30 | paraTypeCharmm on 31 | 32 | 33 | # 1-4 TERMs 34 | 35 | exclude scaled1-4 36 | 1-4scaling 1.0 37 | 38 | 39 | # INPUT FILES 40 | 41 | coordinates deca-ala.pdb 42 | 43 | temperature 300.0 44 | 45 | # OUTPUT FILES 46 | 47 | outputname output/abf 48 | 49 | 50 | # FREQUENCY FOR DUMPING OUTPUT DATA 51 | 52 | outputenergies 1000 53 | outputtiming 1000 54 | outputpressure 1000 55 | restartfreq 1000 56 | XSTFreq 1000 57 | dcdFreq 1000 58 | 59 | 60 | # CUT-OFFs 61 | 62 | hgroupcutoff 2.8 63 | switching on 64 | switchdist 10.0 65 | cutoff 12.0 66 | pairlistdist 14.0 67 | 68 | 69 | # CONSTANT-T 70 | 71 | langevin on 72 | langevintemp 300.0 73 | langevindamping 1.0 74 | 75 | 76 | # MULTIPLE TIME-STEP PROPAGATOR 77 | 78 | timestep 0.5 79 | 80 | 81 | # SHAKE/RATTLE 82 | 83 | rigidbonds none 84 | 85 | 86 | # PARALLELISM 87 | 88 | stepspercycle 16 89 | splitpatch hydrogen 90 | margin 2.0 91 | 92 | 93 | # ABF SECTION 94 | 95 | colvars on 96 | colvarsConfig Distance.in 97 | -------------------------------------------------------------------------------- /NAMD_Colvars/ABF/deca-ala.pdb: -------------------------------------------------------------------------------- 1 | REMARK FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 50000 2 | ATOM 1 N ALA B 1 0.113 -2.288 -1.254 1.00 0.00 BH 3 | ATOM 2 HT2 ALA B 1 -0.779 -1.974 -1.687 1.00 0.00 BH 4 | ATOM 3 HT3 ALA B 1 0.803 -2.829 -1.813 1.00 0.00 BH 5 | ATOM 4 CA ALA B 1 0.767 -1.116 -0.506 1.00 0.00 BH 6 | ATOM 5 HA ALA B 1 1.714 -1.559 -0.234 1.00 0.00 BH 7 | ATOM 6 CB ALA B 1 0.790 0.006 -1.515 1.00 0.00 BH 8 | ATOM 7 HB1 ALA B 1 1.247 0.922 -1.085 1.00 0.00 BH 9 | ATOM 8 HB2 ALA B 1 1.323 -0.411 -2.396 1.00 0.00 BH 10 | ATOM 9 HB3 ALA B 1 -0.176 0.421 -1.873 1.00 0.00 BH 11 | ATOM 10 C ALA B 1 -0.064 -0.634 0.728 1.00 0.00 BH 12 | ATOM 11 O ALA B 1 -1.283 -0.502 0.585 1.00 0.00 BH 13 | ATOM 12 N ALA B 2 0.567 -0.384 1.892 1.00 0.00 BH 14 | ATOM 13 HN ALA B 2 1.558 -0.447 1.979 1.00 0.00 BH 15 | ATOM 14 CA ALA B 2 -0.136 -0.308 3.124 1.00 0.00 BH 16 | ATOM 15 HA ALA B 2 -0.582 -1.269 3.333 1.00 0.00 BH 17 | ATOM 16 CB ALA B 2 0.894 -0.058 4.221 1.00 0.00 BH 18 | ATOM 17 HB1 ALA B 2 0.586 0.170 5.264 1.00 0.00 BH 19 | ATOM 18 HB2 ALA B 2 1.386 -1.043 4.368 1.00 0.00 BH 20 | ATOM 19 HB3 ALA B 2 1.572 0.761 3.896 1.00 0.00 BH 21 | ATOM 20 C ALA B 2 -1.193 0.854 3.162 1.00 0.00 BH 22 | ATOM 21 O ALA B 2 -2.372 0.602 3.566 1.00 0.00 BH 23 | ATOM 22 N ALA B 3 -0.856 2.141 2.875 1.00 0.00 BH 24 | ATOM 23 HN ALA B 3 0.082 2.422 2.689 1.00 0.00 BH 25 | ATOM 24 CA ALA B 3 -1.733 3.280 2.950 1.00 0.00 BH 26 | ATOM 25 HA ALA B 3 -1.997 3.414 3.989 1.00 0.00 BH 27 | ATOM 26 CB ALA B 3 -0.919 4.499 2.477 1.00 0.00 BH 28 | ATOM 27 HB1 ALA B 3 -0.655 4.413 1.401 1.00 0.00 BH 29 | ATOM 28 HB2 ALA B 3 -1.373 5.496 2.661 1.00 0.00 BH 30 | ATOM 29 HB3 ALA B 3 0.046 4.517 3.027 1.00 0.00 BH 31 | ATOM 30 C ALA B 3 -3.066 3.199 2.243 1.00 0.00 BH 32 | ATOM 31 O ALA B 3 -4.119 3.466 2.841 1.00 0.00 BH 33 | ATOM 32 N ALA B 4 -3.071 2.558 1.079 1.00 0.00 BH 34 | ATOM 33 HN ALA B 4 -2.166 2.271 0.776 1.00 0.00 BH 35 | ATOM 34 CA ALA B 4 -4.295 2.275 0.353 1.00 0.00 BH 36 | ATOM 35 HA ALA B 4 -4.896 3.161 0.210 1.00 0.00 BH 37 | ATOM 36 CB ALA B 4 -3.971 1.919 -1.163 1.00 0.00 BH 38 | ATOM 37 HB1 ALA B 4 -3.481 2.802 -1.626 1.00 0.00 BH 39 | ATOM 38 HB2 ALA B 4 -3.239 1.084 -1.214 1.00 0.00 BH 40 | ATOM 39 HB3 ALA B 4 -4.905 1.551 -1.638 1.00 0.00 BH 41 | ATOM 40 C ALA B 4 -5.138 1.148 1.014 1.00 0.00 BH 42 | ATOM 41 O ALA B 4 -6.290 1.290 1.505 1.00 0.00 BH 43 | ATOM 42 N ALA B 5 -4.485 -0.069 0.981 1.00 0.00 BH 44 | ATOM 43 HN ALA B 5 -3.535 -0.144 0.687 1.00 0.00 BH 45 | ATOM 44 CA ALA B 5 -4.953 -1.327 1.563 1.00 0.00 BH 46 | ATOM 45 HA ALA B 5 -5.600 -1.791 0.833 1.00 0.00 BH 47 | ATOM 46 CB ALA B 5 -3.792 -2.416 1.640 1.00 0.00 BH 48 | ATOM 47 HB1 ALA B 5 -3.238 -2.513 0.682 1.00 0.00 BH 49 | ATOM 48 HB2 ALA B 5 -3.051 -2.249 2.451 1.00 0.00 BH 50 | ATOM 49 HB3 ALA B 5 -4.151 -3.455 1.805 1.00 0.00 BH 51 | ATOM 50 C ALA B 5 -5.728 -1.269 2.853 1.00 0.00 BH 52 | ATOM 51 O ALA B 5 -6.821 -1.826 3.026 1.00 0.00 BH 53 | ATOM 52 N ALA B 6 -5.092 -0.721 3.920 1.00 0.00 BH 54 | ATOM 53 HN ALA B 6 -4.250 -0.199 3.808 1.00 0.00 BH 55 | ATOM 54 CA ALA B 6 -5.756 -0.450 5.212 1.00 0.00 BH 56 | ATOM 55 HA ALA B 6 -6.319 -1.344 5.435 1.00 0.00 BH 57 | ATOM 56 CB ALA B 6 -4.701 -0.089 6.243 1.00 0.00 BH 58 | ATOM 57 HB1 ALA B 6 -4.174 0.836 5.923 1.00 0.00 BH 59 | ATOM 58 HB2 ALA B 6 -5.122 -0.006 7.268 1.00 0.00 BH 60 | ATOM 59 HB3 ALA B 6 -4.066 -0.993 6.365 1.00 0.00 BH 61 | ATOM 60 C ALA B 6 -6.839 0.547 5.134 1.00 0.00 BH 62 | ATOM 61 O ALA B 6 -7.796 0.344 5.789 1.00 0.00 BH 63 | ATOM 62 N ALA B 7 -6.709 1.632 4.377 1.00 0.00 BH 64 | ATOM 63 HN ALA B 7 -5.900 1.830 3.830 1.00 0.00 BH 65 | ATOM 64 CA ALA B 7 -7.707 2.606 4.337 1.00 0.00 BH 66 | ATOM 65 HA ALA B 7 -8.028 2.824 5.345 1.00 0.00 BH 67 | ATOM 66 CB ALA B 7 -6.920 3.781 3.934 1.00 0.00 BH 68 | ATOM 67 HB1 ALA B 7 -6.703 3.722 2.846 1.00 0.00 BH 69 | ATOM 68 HB2 ALA B 7 -7.445 4.746 4.096 1.00 0.00 BH 70 | ATOM 69 HB3 ALA B 7 -5.940 3.795 4.458 1.00 0.00 BH 71 | ATOM 70 C ALA B 7 -8.912 2.354 3.463 1.00 0.00 BH 72 | ATOM 71 O ALA B 7 -9.974 2.853 3.663 1.00 0.00 BH 73 | ATOM 72 N ALA B 8 -8.864 1.404 2.514 1.00 0.00 BH 74 | ATOM 73 HN ALA B 8 -7.932 1.244 2.200 1.00 0.00 BH 75 | ATOM 74 CA ALA B 8 -10.008 0.910 1.816 1.00 0.00 BH 76 | ATOM 75 HA ALA B 8 -10.785 1.635 1.621 1.00 0.00 BH 77 | ATOM 76 CB ALA B 8 -9.572 0.291 0.457 1.00 0.00 BH 78 | ATOM 77 HB1 ALA B 8 -10.397 -0.326 0.040 1.00 0.00 BH 79 | ATOM 78 HB2 ALA B 8 -9.311 1.110 -0.247 1.00 0.00 BH 80 | ATOM 79 HB3 ALA B 8 -8.793 -0.479 0.643 1.00 0.00 BH 81 | ATOM 80 C ALA B 8 -10.663 -0.166 2.707 1.00 0.00 BH 82 | ATOM 81 O ALA B 8 -11.882 -0.432 2.666 1.00 0.00 BH 83 | ATOM 82 N ALA B 9 -9.886 -0.789 3.580 1.00 0.00 BH 84 | ATOM 83 HN ALA B 9 -8.904 -0.621 3.609 1.00 0.00 BH 85 | ATOM 84 CA ALA B 9 -10.404 -1.774 4.539 1.00 0.00 BH 86 | ATOM 85 HA ALA B 9 -10.996 -2.532 4.049 1.00 0.00 BH 87 | ATOM 86 CB ALA B 9 -9.238 -2.543 5.191 1.00 0.00 BH 88 | ATOM 87 HB1 ALA B 9 -8.806 -3.097 4.331 1.00 0.00 BH 89 | ATOM 88 HB2 ALA B 9 -8.467 -1.819 5.532 1.00 0.00 BH 90 | ATOM 89 HB3 ALA B 9 -9.463 -3.262 6.007 1.00 0.00 BH 91 | ATOM 90 C ALA B 9 -11.212 -1.063 5.618 1.00 0.00 BH 92 | ATOM 91 O ALA B 9 -12.370 -1.417 5.769 1.00 0.00 BH 93 | ATOM 92 C ALA B 10 -11.957 1.980 7.072 1.00 0.00 BH 94 | ATOM 93 O ALA B 10 -11.964 3.008 7.760 1.00 0.00 BH 95 | ATOM 94 NT ALA B 10 -12.813 1.968 5.971 1.00 0.00 BH 96 | ATOM 95 HT1 ALA B 10 -13.399 2.748 5.755 1.00 0.00 BH 97 | ATOM 96 HT2 ALA B 10 -12.618 1.237 5.316 1.00 0.00 BH 98 | ATOM 97 N ALA B 10 -10.690 0.020 6.213 1.00 0.00 BH 99 | ATOM 98 HN ALA B 10 -9.720 0.133 6.012 1.00 0.00 BH 100 | ATOM 99 CA ALA B 10 -11.166 0.664 7.402 1.00 0.00 BH 101 | ATOM 100 HA ALA B 10 -11.936 0.058 7.856 1.00 0.00 BH 102 | ATOM 101 CB ALA B 10 -10.058 0.920 8.404 1.00 0.00 BH 103 | ATOM 102 HB1 ALA B 10 -9.202 1.387 7.871 1.00 0.00 BH 104 | ATOM 103 HB2 ALA B 10 -10.427 1.550 9.242 1.00 0.00 BH 105 | ATOM 104 HB3 ALA B 10 -9.603 -0.048 8.702 1.00 0.00 BH 106 | END 107 | -------------------------------------------------------------------------------- /NAMD_Colvars/ABF/deca-ala.psf: -------------------------------------------------------------------------------- 1 | PSF 2 | 3 | 1 !NTITLE 4 | REMARKS original generated structure x-plor psf file 5 | 6 | 104 !NATOM 7 | 1 BH 1 ALA N NH3 -0.620000 14.0070 0 8 | 2 BH 1 ALA HT2 HC 0.310000 1.0080 0 9 | 3 BH 1 ALA HT3 HC 0.310000 1.0080 0 10 | 4 BH 1 ALA CA CT1 -0.100000 12.0110 0 11 | 5 BH 1 ALA HA HB 0.100000 1.0080 0 12 | 6 BH 1 ALA CB CT3 -0.270000 12.0110 0 13 | 7 BH 1 ALA HB1 HA 0.090000 1.0080 0 14 | 8 BH 1 ALA HB2 HA 0.090000 1.0080 0 15 | 9 BH 1 ALA HB3 HA 0.090000 1.0080 0 16 | 10 BH 1 ALA C C 0.510000 12.0110 0 17 | 11 BH 1 ALA O O -0.510000 15.9990 0 18 | 12 BH 2 ALA N NH1 -0.470000 14.0070 0 19 | 13 BH 2 ALA HN H 0.310000 1.0080 0 20 | 14 BH 2 ALA CA CT1 0.070000 12.0110 0 21 | 15 BH 2 ALA HA HB 0.090000 1.0080 0 22 | 16 BH 2 ALA CB CT3 -0.270000 12.0110 0 23 | 17 BH 2 ALA HB1 HA 0.090000 1.0080 0 24 | 18 BH 2 ALA HB2 HA 0.090000 1.0080 0 25 | 19 BH 2 ALA HB3 HA 0.090000 1.0080 0 26 | 20 BH 2 ALA C C 0.510000 12.0110 0 27 | 21 BH 2 ALA O O -0.510000 15.9990 0 28 | 22 BH 3 ALA N NH1 -0.470000 14.0070 0 29 | 23 BH 3 ALA HN H 0.310000 1.0080 0 30 | 24 BH 3 ALA CA CT1 0.070000 12.0110 0 31 | 25 BH 3 ALA HA HB 0.090000 1.0080 0 32 | 26 BH 3 ALA CB CT3 -0.270000 12.0110 0 33 | 27 BH 3 ALA HB1 HA 0.090000 1.0080 0 34 | 28 BH 3 ALA HB2 HA 0.090000 1.0080 0 35 | 29 BH 3 ALA HB3 HA 0.090000 1.0080 0 36 | 30 BH 3 ALA C C 0.510000 12.0110 0 37 | 31 BH 3 ALA O O -0.510000 15.9990 0 38 | 32 BH 4 ALA N NH1 -0.470000 14.0070 0 39 | 33 BH 4 ALA HN H 0.310000 1.0080 0 40 | 34 BH 4 ALA CA CT1 0.070000 12.0110 0 41 | 35 BH 4 ALA HA HB 0.090000 1.0080 0 42 | 36 BH 4 ALA CB CT3 -0.270000 12.0110 0 43 | 37 BH 4 ALA HB1 HA 0.090000 1.0080 0 44 | 38 BH 4 ALA HB2 HA 0.090000 1.0080 0 45 | 39 BH 4 ALA HB3 HA 0.090000 1.0080 0 46 | 40 BH 4 ALA C C 0.510000 12.0110 0 47 | 41 BH 4 ALA O O -0.510000 15.9990 0 48 | 42 BH 5 ALA N NH1 -0.470000 14.0070 0 49 | 43 BH 5 ALA HN H 0.310000 1.0080 0 50 | 44 BH 5 ALA CA CT1 0.070000 12.0110 0 51 | 45 BH 5 ALA HA HB 0.090000 1.0080 0 52 | 46 BH 5 ALA CB CT3 -0.270000 12.0110 0 53 | 47 BH 5 ALA HB1 HA 0.090000 1.0080 0 54 | 48 BH 5 ALA HB2 HA 0.090000 1.0080 0 55 | 49 BH 5 ALA HB3 HA 0.090000 1.0080 0 56 | 50 BH 5 ALA C C 0.510000 12.0110 0 57 | 51 BH 5 ALA O O -0.510000 15.9990 0 58 | 52 BH 6 ALA N NH1 -0.470000 14.0070 0 59 | 53 BH 6 ALA HN H 0.310000 1.0080 0 60 | 54 BH 6 ALA CA CT1 0.070000 12.0110 0 61 | 55 BH 6 ALA HA HB 0.090000 1.0080 0 62 | 56 BH 6 ALA CB CT3 -0.270000 12.0110 0 63 | 57 BH 6 ALA HB1 HA 0.090000 1.0080 0 64 | 58 BH 6 ALA HB2 HA 0.090000 1.0080 0 65 | 59 BH 6 ALA HB3 HA 0.090000 1.0080 0 66 | 60 BH 6 ALA C C 0.510000 12.0110 0 67 | 61 BH 6 ALA O O -0.510000 15.9990 0 68 | 62 BH 7 ALA N NH1 -0.470000 14.0070 0 69 | 63 BH 7 ALA HN H 0.310000 1.0080 0 70 | 64 BH 7 ALA CA CT1 0.070000 12.0110 0 71 | 65 BH 7 ALA HA HB 0.090000 1.0080 0 72 | 66 BH 7 ALA CB CT3 -0.270000 12.0110 0 73 | 67 BH 7 ALA HB1 HA 0.090000 1.0080 0 74 | 68 BH 7 ALA HB2 HA 0.090000 1.0080 0 75 | 69 BH 7 ALA HB3 HA 0.090000 1.0080 0 76 | 70 BH 7 ALA C C 0.510000 12.0110 0 77 | 71 BH 7 ALA O O -0.510000 15.9990 0 78 | 72 BH 8 ALA N NH1 -0.470000 14.0070 0 79 | 73 BH 8 ALA HN H 0.310000 1.0080 0 80 | 74 BH 8 ALA CA CT1 0.070000 12.0110 0 81 | 75 BH 8 ALA HA HB 0.090000 1.0080 0 82 | 76 BH 8 ALA CB CT3 -0.270000 12.0110 0 83 | 77 BH 8 ALA HB1 HA 0.090000 1.0080 0 84 | 78 BH 8 ALA HB2 HA 0.090000 1.0080 0 85 | 79 BH 8 ALA HB3 HA 0.090000 1.0080 0 86 | 80 BH 8 ALA C C 0.510000 12.0110 0 87 | 81 BH 8 ALA O O -0.510000 15.9990 0 88 | 82 BH 9 ALA N NH1 -0.470000 14.0070 0 89 | 83 BH 9 ALA HN H 0.310000 1.0080 0 90 | 84 BH 9 ALA CA CT1 0.070000 12.0110 0 91 | 85 BH 9 ALA HA HB 0.090000 1.0080 0 92 | 86 BH 9 ALA CB CT3 -0.270000 12.0110 0 93 | 87 BH 9 ALA HB1 HA 0.090000 1.0080 0 94 | 88 BH 9 ALA HB2 HA 0.090000 1.0080 0 95 | 89 BH 9 ALA HB3 HA 0.090000 1.0080 0 96 | 90 BH 9 ALA C C 0.510000 12.0110 0 97 | 91 BH 9 ALA O O -0.510000 15.9990 0 98 | 92 BH 10 ALA C CC 0.550000 12.0110 0 99 | 93 BH 10 ALA O O -0.550000 15.9990 0 100 | 94 BH 10 ALA NT NH2 -0.620000 14.0070 0 101 | 95 BH 10 ALA HT1 H 0.320000 1.0080 0 102 | 96 BH 10 ALA HT2 H 0.300000 1.0080 0 103 | 97 BH 10 ALA N NH1 -0.470000 14.0070 0 104 | 98 BH 10 ALA HN H 0.310000 1.0080 0 105 | 99 BH 10 ALA CA CT1 0.070000 12.0110 0 106 | 100 BH 10 ALA HA HB 0.090000 1.0080 0 107 | 101 BH 10 ALA CB CT3 -0.270000 12.0110 0 108 | 102 BH 10 ALA HB1 HA 0.090000 1.0080 0 109 | 103 BH 10 ALA HB2 HA 0.090000 1.0080 0 110 | 104 BH 10 ALA HB3 HA 0.090000 1.0080 0 111 | 112 | 103 !NBOND: bonds 113 | 1 4 2 1 3 1 4 5 114 | 6 4 6 7 6 8 6 9 115 | 10 4 10 12 11 10 12 13 116 | 12 14 14 15 16 14 16 17 117 | 16 18 16 19 20 14 20 22 118 | 21 20 22 23 22 24 24 25 119 | 26 24 26 27 26 28 26 29 120 | 30 24 30 32 31 30 32 33 121 | 32 34 34 35 36 34 36 37 122 | 36 38 36 39 40 34 40 42 123 | 41 40 42 43 42 44 44 45 124 | 46 44 46 47 46 48 46 49 125 | 50 44 50 52 51 50 52 53 126 | 52 54 54 55 56 54 56 57 127 | 56 58 56 59 60 54 60 62 128 | 61 60 62 63 62 64 64 65 129 | 66 64 66 67 66 68 66 69 130 | 70 64 70 72 71 70 72 73 131 | 72 74 74 75 76 74 76 77 132 | 76 78 76 79 80 74 80 82 133 | 81 80 82 83 82 84 84 85 134 | 86 84 86 87 86 88 86 89 135 | 90 84 90 97 91 90 92 94 136 | 92 99 93 92 94 95 94 96 137 | 97 98 97 99 99 100 101 99 138 | 101 102 101 103 101 104 139 | 140 | 183 !NTHETA: angles 141 | 1 4 5 1 4 10 2 1 4 142 | 2 1 3 3 1 4 4 10 11 143 | 4 10 12 4 6 9 4 6 8 144 | 4 6 7 6 4 5 6 4 10 145 | 6 4 1 7 6 9 7 6 8 146 | 8 6 9 10 4 5 12 14 15 147 | 12 14 20 12 10 11 13 12 10 148 | 13 12 14 14 20 21 14 20 22 149 | 14 16 19 14 16 18 14 16 17 150 | 14 12 10 16 14 15 16 14 20 151 | 16 14 12 17 16 19 17 16 18 152 | 18 16 19 20 14 15 22 24 25 153 | 22 24 30 22 20 21 23 22 20 154 | 23 22 24 24 30 31 24 30 32 155 | 24 26 29 24 26 28 24 26 27 156 | 24 22 20 26 24 25 26 24 30 157 | 26 24 22 27 26 29 27 26 28 158 | 28 26 29 30 24 25 32 34 35 159 | 32 34 40 32 30 31 33 32 30 160 | 33 32 34 34 40 41 34 40 42 161 | 34 36 39 34 36 38 34 36 37 162 | 34 32 30 36 34 35 36 34 40 163 | 36 34 32 37 36 39 37 36 38 164 | 38 36 39 40 34 35 42 44 45 165 | 42 44 50 42 40 41 43 42 40 166 | 43 42 44 44 50 51 44 50 52 167 | 44 46 49 44 46 48 44 46 47 168 | 44 42 40 46 44 45 46 44 50 169 | 46 44 42 47 46 49 47 46 48 170 | 48 46 49 50 44 45 52 54 55 171 | 52 54 60 52 50 51 53 52 50 172 | 53 52 54 54 60 61 54 60 62 173 | 54 56 59 54 56 58 54 56 57 174 | 54 52 50 56 54 55 56 54 60 175 | 56 54 52 57 56 59 57 56 58 176 | 58 56 59 60 54 55 62 64 65 177 | 62 64 70 62 60 61 63 62 60 178 | 63 62 64 64 70 71 64 70 72 179 | 64 66 69 64 66 68 64 66 67 180 | 64 62 60 66 64 65 66 64 70 181 | 66 64 62 67 66 69 67 66 68 182 | 68 66 69 70 64 65 72 74 75 183 | 72 74 80 72 70 71 73 72 70 184 | 73 72 74 74 80 81 74 80 82 185 | 74 76 79 74 76 78 74 76 77 186 | 74 72 70 76 74 75 76 74 80 187 | 76 74 72 77 76 79 77 76 78 188 | 78 76 79 80 74 75 82 84 85 189 | 82 84 90 82 80 81 83 82 80 190 | 83 82 84 84 90 91 84 90 97 191 | 84 86 89 84 86 88 84 86 87 192 | 84 82 80 86 84 85 86 84 90 193 | 86 84 82 87 86 89 87 86 88 194 | 88 86 89 90 84 85 92 99 100 195 | 92 94 96 92 94 95 94 92 93 196 | 94 92 99 95 94 96 97 99 100 197 | 97 99 92 97 90 91 98 97 90 198 | 98 97 99 99 101 104 99 101 103 199 | 99 101 102 99 97 90 99 92 93 200 | 101 99 100 101 99 92 101 99 97 201 | 102 101 104 102 101 103 103 101 104 202 | 203 | 251 !NPHI: dihedrals 204 | 1 4 6 7 1 4 6 8 205 | 1 4 6 9 1 4 10 12 206 | 1 4 10 11 2 1 4 6 207 | 2 1 4 10 2 1 4 5 208 | 3 1 4 6 3 1 4 10 209 | 3 1 4 5 4 10 12 13 210 | 4 10 12 14 5 4 6 7 211 | 5 4 6 8 5 4 6 9 212 | 5 4 10 12 5 4 10 11 213 | 6 4 10 12 6 4 10 11 214 | 7 6 4 10 8 6 4 10 215 | 9 6 4 10 10 12 14 16 216 | 10 12 14 20 10 12 14 15 217 | 11 10 12 13 11 10 12 14 218 | 12 14 16 17 12 14 16 18 219 | 12 14 16 19 12 14 20 22 220 | 12 14 20 21 13 12 14 16 221 | 13 12 14 20 13 12 14 15 222 | 14 20 22 23 14 20 22 24 223 | 15 14 16 17 15 14 16 18 224 | 15 14 16 19 15 14 20 22 225 | 15 14 20 21 16 14 20 22 226 | 16 14 20 21 17 16 14 20 227 | 18 16 14 20 19 16 14 20 228 | 20 22 24 26 20 22 24 30 229 | 20 22 24 25 21 20 22 23 230 | 21 20 22 24 22 24 26 27 231 | 22 24 26 28 22 24 26 29 232 | 22 24 30 32 22 24 30 31 233 | 23 22 24 26 23 22 24 30 234 | 23 22 24 25 24 30 32 33 235 | 24 30 32 34 25 24 26 27 236 | 25 24 26 28 25 24 26 29 237 | 25 24 30 32 25 24 30 31 238 | 26 24 30 32 26 24 30 31 239 | 27 26 24 30 28 26 24 30 240 | 29 26 24 30 30 32 34 36 241 | 30 32 34 40 30 32 34 35 242 | 31 30 32 33 31 30 32 34 243 | 32 34 36 37 32 34 36 38 244 | 32 34 36 39 32 34 40 42 245 | 32 34 40 41 33 32 34 36 246 | 33 32 34 40 33 32 34 35 247 | 34 40 42 43 34 40 42 44 248 | 35 34 36 37 35 34 36 38 249 | 35 34 36 39 35 34 40 42 250 | 35 34 40 41 36 34 40 42 251 | 36 34 40 41 37 36 34 40 252 | 38 36 34 40 39 36 34 40 253 | 40 42 44 46 40 42 44 50 254 | 40 42 44 45 41 40 42 43 255 | 41 40 42 44 42 44 46 47 256 | 42 44 46 48 42 44 46 49 257 | 42 44 50 52 42 44 50 51 258 | 43 42 44 46 43 42 44 50 259 | 43 42 44 45 44 50 52 53 260 | 44 50 52 54 45 44 46 47 261 | 45 44 46 48 45 44 46 49 262 | 45 44 50 52 45 44 50 51 263 | 46 44 50 52 46 44 50 51 264 | 47 46 44 50 48 46 44 50 265 | 49 46 44 50 50 52 54 56 266 | 50 52 54 60 50 52 54 55 267 | 51 50 52 53 51 50 52 54 268 | 52 54 56 57 52 54 56 58 269 | 52 54 56 59 52 54 60 62 270 | 52 54 60 61 53 52 54 56 271 | 53 52 54 60 53 52 54 55 272 | 54 60 62 63 54 60 62 64 273 | 55 54 56 57 55 54 56 58 274 | 55 54 56 59 55 54 60 62 275 | 55 54 60 61 56 54 60 62 276 | 56 54 60 61 57 56 54 60 277 | 58 56 54 60 59 56 54 60 278 | 60 62 64 66 60 62 64 70 279 | 60 62 64 65 61 60 62 63 280 | 61 60 62 64 62 64 66 67 281 | 62 64 66 68 62 64 66 69 282 | 62 64 70 72 62 64 70 71 283 | 63 62 64 66 63 62 64 70 284 | 63 62 64 65 64 70 72 73 285 | 64 70 72 74 65 64 66 67 286 | 65 64 66 68 65 64 66 69 287 | 65 64 70 72 65 64 70 71 288 | 66 64 70 72 66 64 70 71 289 | 67 66 64 70 68 66 64 70 290 | 69 66 64 70 70 72 74 76 291 | 70 72 74 80 70 72 74 75 292 | 71 70 72 73 71 70 72 74 293 | 72 74 76 77 72 74 76 78 294 | 72 74 76 79 72 74 80 82 295 | 72 74 80 81 73 72 74 76 296 | 73 72 74 80 73 72 74 75 297 | 74 80 82 83 74 80 82 84 298 | 75 74 76 77 75 74 76 78 299 | 75 74 76 79 75 74 80 82 300 | 75 74 80 81 76 74 80 82 301 | 76 74 80 81 77 76 74 80 302 | 78 76 74 80 79 76 74 80 303 | 80 82 84 86 80 82 84 90 304 | 80 82 84 85 81 80 82 83 305 | 81 80 82 84 82 84 86 87 306 | 82 84 86 88 82 84 86 89 307 | 82 84 90 97 82 84 90 91 308 | 83 82 84 86 83 82 84 90 309 | 83 82 84 85 84 90 97 98 310 | 84 90 97 99 85 84 86 87 311 | 85 84 86 88 85 84 86 89 312 | 85 84 90 97 85 84 90 91 313 | 86 84 90 97 86 84 90 91 314 | 87 86 84 90 88 86 84 90 315 | 89 86 84 90 90 97 99 101 316 | 90 97 99 92 90 97 99 100 317 | 91 90 97 98 91 90 97 99 318 | 92 99 101 102 92 99 101 103 319 | 92 99 101 104 92 99 97 98 320 | 93 92 94 95 93 92 94 96 321 | 93 92 99 101 93 92 99 97 322 | 93 92 99 100 94 92 99 101 323 | 94 92 99 97 94 92 99 100 324 | 95 94 92 99 96 94 92 99 325 | 97 99 101 102 97 99 101 103 326 | 97 99 101 104 98 97 99 101 327 | 98 97 99 100 99 92 94 96 328 | 100 99 101 102 100 99 101 103 329 | 100 99 101 104 330 | 331 | 22 !NIMPHI: impropers 332 | 10 4 12 11 12 10 14 13 333 | 20 14 22 21 22 20 24 23 334 | 30 24 32 31 32 30 34 33 335 | 40 34 42 41 42 40 44 43 336 | 50 44 52 51 52 50 54 53 337 | 60 54 62 61 62 60 64 63 338 | 70 64 72 71 72 70 74 73 339 | 80 74 82 81 82 80 84 83 340 | 90 84 97 91 92 94 99 93 341 | 92 99 94 93 94 92 95 96 342 | 94 92 96 95 97 90 99 98 343 | 344 | 0 !NDON: donors 345 | 346 | 347 | 0 !NACC: acceptors 348 | 349 | 350 | 0 !NNB 351 | 352 | 0 0 0 0 0 0 0 0 353 | 0 0 0 0 0 0 0 0 354 | 0 0 0 0 0 0 0 0 355 | 0 0 0 0 0 0 0 0 356 | 0 0 0 0 0 0 0 0 357 | 0 0 0 0 0 0 0 0 358 | 0 0 0 0 0 0 0 0 359 | 0 0 0 0 0 0 0 0 360 | 0 0 0 0 0 0 0 0 361 | 0 0 0 0 0 0 0 0 362 | 0 0 0 0 0 0 0 0 363 | 0 0 0 0 0 0 0 0 364 | 0 0 0 0 0 0 0 0 365 | 366 | 367 | 1 0 !NGRP 368 | 0 0 0 369 | 370 | -------------------------------------------------------------------------------- /NAMD_Colvars/WTM-eABF/Distance.in: -------------------------------------------------------------------------------- 1 | colvarsTrajFrequency 1000 2 | colvarsRestartFrequency 50000 3 | 4 | colvar { 5 | name AtomDistance 6 | 7 | width 0.1 8 | 9 | lowerboundary 12.0 10 | upperboundary 32.0 11 | 12 | lowerwallconstant 10.0 13 | upperwallconstant 10.0 14 | 15 | extendedLagrangian on 16 | extendedFluctuation 0.1 17 | 18 | subtractAppliedForce on 19 | expandBoundaries on 20 | 21 | distance { 22 | group1 { 23 | atomnumbers { 10 } 24 | } 25 | group2 { 26 | atomnumbers { 92 } 27 | } 28 | } 29 | } 30 | 31 | 32 | abf { 33 | colvars AtomDistance 34 | fullSamples 500 35 | } 36 | 37 | metadynamics { 38 | colvars AtomDistance 39 | hillWeight 0.1 40 | hillWidth 3 41 | wellTempered on 42 | biasTemperature 4000 43 | } -------------------------------------------------------------------------------- /NAMD_Colvars/WTM-eABF/abf.conf: -------------------------------------------------------------------------------- 1 | ################################################## 2 | ################################################## 3 | # 4 | # ABF calculation 5 | # 6 | # Deca-alanine 7 | # 8 | ################################################## 9 | ################################################## 10 | 11 | 12 | ################################################## 13 | # MD SECTION 14 | ################################################## 15 | 16 | 17 | # NUMBER OF MD-STEPS 18 | 19 | numsteps 20000000 20 | 21 | 22 | # TOPOLOGY 23 | 24 | structure deca-ala.psf 25 | 26 | 27 | # FORCE FIELD 28 | 29 | parameters par_all22_prot.inp 30 | paraTypeCharmm on 31 | 32 | 33 | # 1-4 TERMs 34 | 35 | exclude scaled1-4 36 | 1-4scaling 1.0 37 | 38 | 39 | # INPUT FILES 40 | 41 | coordinates deca-ala.pdb 42 | 43 | temperature 300.0 44 | 45 | # OUTPUT FILES 46 | 47 | outputname output/abf 48 | 49 | 50 | # FREQUENCY FOR DUMPING OUTPUT DATA 51 | 52 | outputenergies 1000 53 | outputtiming 1000 54 | outputpressure 1000 55 | restartfreq 1000 56 | XSTFreq 1000 57 | dcdFreq 1000 58 | 59 | 60 | # CUT-OFFs 61 | 62 | hgroupcutoff 2.8 63 | switching on 64 | switchdist 10.0 65 | cutoff 12.0 66 | pairlistdist 14.0 67 | 68 | 69 | # CONSTANT-T 70 | 71 | langevin on 72 | langevintemp 300.0 73 | langevindamping 1.0 74 | 75 | 76 | # MULTIPLE TIME-STEP PROPAGATOR 77 | 78 | timestep 0.5 79 | 80 | 81 | # SHAKE/RATTLE 82 | 83 | rigidbonds none 84 | 85 | 86 | # PARALLELISM 87 | 88 | stepspercycle 16 89 | splitpatch hydrogen 90 | margin 2.0 91 | 92 | 93 | # ABF SECTION 94 | 95 | colvars on 96 | colvarsConfig Distance.in 97 | -------------------------------------------------------------------------------- /NAMD_Colvars/WTM-eABF/deca-ala.pdb: -------------------------------------------------------------------------------- 1 | REMARK FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 50000 2 | ATOM 1 N ALA B 1 0.113 -2.288 -1.254 1.00 0.00 BH 3 | ATOM 2 HT2 ALA B 1 -0.779 -1.974 -1.687 1.00 0.00 BH 4 | ATOM 3 HT3 ALA B 1 0.803 -2.829 -1.813 1.00 0.00 BH 5 | ATOM 4 CA ALA B 1 0.767 -1.116 -0.506 1.00 0.00 BH 6 | ATOM 5 HA ALA B 1 1.714 -1.559 -0.234 1.00 0.00 BH 7 | ATOM 6 CB ALA B 1 0.790 0.006 -1.515 1.00 0.00 BH 8 | ATOM 7 HB1 ALA B 1 1.247 0.922 -1.085 1.00 0.00 BH 9 | ATOM 8 HB2 ALA B 1 1.323 -0.411 -2.396 1.00 0.00 BH 10 | ATOM 9 HB3 ALA B 1 -0.176 0.421 -1.873 1.00 0.00 BH 11 | ATOM 10 C ALA B 1 -0.064 -0.634 0.728 1.00 0.00 BH 12 | ATOM 11 O ALA B 1 -1.283 -0.502 0.585 1.00 0.00 BH 13 | ATOM 12 N ALA B 2 0.567 -0.384 1.892 1.00 0.00 BH 14 | ATOM 13 HN ALA B 2 1.558 -0.447 1.979 1.00 0.00 BH 15 | ATOM 14 CA ALA B 2 -0.136 -0.308 3.124 1.00 0.00 BH 16 | ATOM 15 HA ALA B 2 -0.582 -1.269 3.333 1.00 0.00 BH 17 | ATOM 16 CB ALA B 2 0.894 -0.058 4.221 1.00 0.00 BH 18 | ATOM 17 HB1 ALA B 2 0.586 0.170 5.264 1.00 0.00 BH 19 | ATOM 18 HB2 ALA B 2 1.386 -1.043 4.368 1.00 0.00 BH 20 | ATOM 19 HB3 ALA B 2 1.572 0.761 3.896 1.00 0.00 BH 21 | ATOM 20 C ALA B 2 -1.193 0.854 3.162 1.00 0.00 BH 22 | ATOM 21 O ALA B 2 -2.372 0.602 3.566 1.00 0.00 BH 23 | ATOM 22 N ALA B 3 -0.856 2.141 2.875 1.00 0.00 BH 24 | ATOM 23 HN ALA B 3 0.082 2.422 2.689 1.00 0.00 BH 25 | ATOM 24 CA ALA B 3 -1.733 3.280 2.950 1.00 0.00 BH 26 | ATOM 25 HA ALA B 3 -1.997 3.414 3.989 1.00 0.00 BH 27 | ATOM 26 CB ALA B 3 -0.919 4.499 2.477 1.00 0.00 BH 28 | ATOM 27 HB1 ALA B 3 -0.655 4.413 1.401 1.00 0.00 BH 29 | ATOM 28 HB2 ALA B 3 -1.373 5.496 2.661 1.00 0.00 BH 30 | ATOM 29 HB3 ALA B 3 0.046 4.517 3.027 1.00 0.00 BH 31 | ATOM 30 C ALA B 3 -3.066 3.199 2.243 1.00 0.00 BH 32 | ATOM 31 O ALA B 3 -4.119 3.466 2.841 1.00 0.00 BH 33 | ATOM 32 N ALA B 4 -3.071 2.558 1.079 1.00 0.00 BH 34 | ATOM 33 HN ALA B 4 -2.166 2.271 0.776 1.00 0.00 BH 35 | ATOM 34 CA ALA B 4 -4.295 2.275 0.353 1.00 0.00 BH 36 | ATOM 35 HA ALA B 4 -4.896 3.161 0.210 1.00 0.00 BH 37 | ATOM 36 CB ALA B 4 -3.971 1.919 -1.163 1.00 0.00 BH 38 | ATOM 37 HB1 ALA B 4 -3.481 2.802 -1.626 1.00 0.00 BH 39 | ATOM 38 HB2 ALA B 4 -3.239 1.084 -1.214 1.00 0.00 BH 40 | ATOM 39 HB3 ALA B 4 -4.905 1.551 -1.638 1.00 0.00 BH 41 | ATOM 40 C ALA B 4 -5.138 1.148 1.014 1.00 0.00 BH 42 | ATOM 41 O ALA B 4 -6.290 1.290 1.505 1.00 0.00 BH 43 | ATOM 42 N ALA B 5 -4.485 -0.069 0.981 1.00 0.00 BH 44 | ATOM 43 HN ALA B 5 -3.535 -0.144 0.687 1.00 0.00 BH 45 | ATOM 44 CA ALA B 5 -4.953 -1.327 1.563 1.00 0.00 BH 46 | ATOM 45 HA ALA B 5 -5.600 -1.791 0.833 1.00 0.00 BH 47 | ATOM 46 CB ALA B 5 -3.792 -2.416 1.640 1.00 0.00 BH 48 | ATOM 47 HB1 ALA B 5 -3.238 -2.513 0.682 1.00 0.00 BH 49 | ATOM 48 HB2 ALA B 5 -3.051 -2.249 2.451 1.00 0.00 BH 50 | ATOM 49 HB3 ALA B 5 -4.151 -3.455 1.805 1.00 0.00 BH 51 | ATOM 50 C ALA B 5 -5.728 -1.269 2.853 1.00 0.00 BH 52 | ATOM 51 O ALA B 5 -6.821 -1.826 3.026 1.00 0.00 BH 53 | ATOM 52 N ALA B 6 -5.092 -0.721 3.920 1.00 0.00 BH 54 | ATOM 53 HN ALA B 6 -4.250 -0.199 3.808 1.00 0.00 BH 55 | ATOM 54 CA ALA B 6 -5.756 -0.450 5.212 1.00 0.00 BH 56 | ATOM 55 HA ALA B 6 -6.319 -1.344 5.435 1.00 0.00 BH 57 | ATOM 56 CB ALA B 6 -4.701 -0.089 6.243 1.00 0.00 BH 58 | ATOM 57 HB1 ALA B 6 -4.174 0.836 5.923 1.00 0.00 BH 59 | ATOM 58 HB2 ALA B 6 -5.122 -0.006 7.268 1.00 0.00 BH 60 | ATOM 59 HB3 ALA B 6 -4.066 -0.993 6.365 1.00 0.00 BH 61 | ATOM 60 C ALA B 6 -6.839 0.547 5.134 1.00 0.00 BH 62 | ATOM 61 O ALA B 6 -7.796 0.344 5.789 1.00 0.00 BH 63 | ATOM 62 N ALA B 7 -6.709 1.632 4.377 1.00 0.00 BH 64 | ATOM 63 HN ALA B 7 -5.900 1.830 3.830 1.00 0.00 BH 65 | ATOM 64 CA ALA B 7 -7.707 2.606 4.337 1.00 0.00 BH 66 | ATOM 65 HA ALA B 7 -8.028 2.824 5.345 1.00 0.00 BH 67 | ATOM 66 CB ALA B 7 -6.920 3.781 3.934 1.00 0.00 BH 68 | ATOM 67 HB1 ALA B 7 -6.703 3.722 2.846 1.00 0.00 BH 69 | ATOM 68 HB2 ALA B 7 -7.445 4.746 4.096 1.00 0.00 BH 70 | ATOM 69 HB3 ALA B 7 -5.940 3.795 4.458 1.00 0.00 BH 71 | ATOM 70 C ALA B 7 -8.912 2.354 3.463 1.00 0.00 BH 72 | ATOM 71 O ALA B 7 -9.974 2.853 3.663 1.00 0.00 BH 73 | ATOM 72 N ALA B 8 -8.864 1.404 2.514 1.00 0.00 BH 74 | ATOM 73 HN ALA B 8 -7.932 1.244 2.200 1.00 0.00 BH 75 | ATOM 74 CA ALA B 8 -10.008 0.910 1.816 1.00 0.00 BH 76 | ATOM 75 HA ALA B 8 -10.785 1.635 1.621 1.00 0.00 BH 77 | ATOM 76 CB ALA B 8 -9.572 0.291 0.457 1.00 0.00 BH 78 | ATOM 77 HB1 ALA B 8 -10.397 -0.326 0.040 1.00 0.00 BH 79 | ATOM 78 HB2 ALA B 8 -9.311 1.110 -0.247 1.00 0.00 BH 80 | ATOM 79 HB3 ALA B 8 -8.793 -0.479 0.643 1.00 0.00 BH 81 | ATOM 80 C ALA B 8 -10.663 -0.166 2.707 1.00 0.00 BH 82 | ATOM 81 O ALA B 8 -11.882 -0.432 2.666 1.00 0.00 BH 83 | ATOM 82 N ALA B 9 -9.886 -0.789 3.580 1.00 0.00 BH 84 | ATOM 83 HN ALA B 9 -8.904 -0.621 3.609 1.00 0.00 BH 85 | ATOM 84 CA ALA B 9 -10.404 -1.774 4.539 1.00 0.00 BH 86 | ATOM 85 HA ALA B 9 -10.996 -2.532 4.049 1.00 0.00 BH 87 | ATOM 86 CB ALA B 9 -9.238 -2.543 5.191 1.00 0.00 BH 88 | ATOM 87 HB1 ALA B 9 -8.806 -3.097 4.331 1.00 0.00 BH 89 | ATOM 88 HB2 ALA B 9 -8.467 -1.819 5.532 1.00 0.00 BH 90 | ATOM 89 HB3 ALA B 9 -9.463 -3.262 6.007 1.00 0.00 BH 91 | ATOM 90 C ALA B 9 -11.212 -1.063 5.618 1.00 0.00 BH 92 | ATOM 91 O ALA B 9 -12.370 -1.417 5.769 1.00 0.00 BH 93 | ATOM 92 C ALA B 10 -11.957 1.980 7.072 1.00 0.00 BH 94 | ATOM 93 O ALA B 10 -11.964 3.008 7.760 1.00 0.00 BH 95 | ATOM 94 NT ALA B 10 -12.813 1.968 5.971 1.00 0.00 BH 96 | ATOM 95 HT1 ALA B 10 -13.399 2.748 5.755 1.00 0.00 BH 97 | ATOM 96 HT2 ALA B 10 -12.618 1.237 5.316 1.00 0.00 BH 98 | ATOM 97 N ALA B 10 -10.690 0.020 6.213 1.00 0.00 BH 99 | ATOM 98 HN ALA B 10 -9.720 0.133 6.012 1.00 0.00 BH 100 | ATOM 99 CA ALA B 10 -11.166 0.664 7.402 1.00 0.00 BH 101 | ATOM 100 HA ALA B 10 -11.936 0.058 7.856 1.00 0.00 BH 102 | ATOM 101 CB ALA B 10 -10.058 0.920 8.404 1.00 0.00 BH 103 | ATOM 102 HB1 ALA B 10 -9.202 1.387 7.871 1.00 0.00 BH 104 | ATOM 103 HB2 ALA B 10 -10.427 1.550 9.242 1.00 0.00 BH 105 | ATOM 104 HB3 ALA B 10 -9.603 -0.048 8.702 1.00 0.00 BH 106 | END 107 | -------------------------------------------------------------------------------- /NAMD_Colvars/WTM-eABF/deca-ala.psf: -------------------------------------------------------------------------------- 1 | PSF 2 | 3 | 1 !NTITLE 4 | REMARKS original generated structure x-plor psf file 5 | 6 | 104 !NATOM 7 | 1 BH 1 ALA N NH3 -0.620000 14.0070 0 8 | 2 BH 1 ALA HT2 HC 0.310000 1.0080 0 9 | 3 BH 1 ALA HT3 HC 0.310000 1.0080 0 10 | 4 BH 1 ALA CA CT1 -0.100000 12.0110 0 11 | 5 BH 1 ALA HA HB 0.100000 1.0080 0 12 | 6 BH 1 ALA CB CT3 -0.270000 12.0110 0 13 | 7 BH 1 ALA HB1 HA 0.090000 1.0080 0 14 | 8 BH 1 ALA HB2 HA 0.090000 1.0080 0 15 | 9 BH 1 ALA HB3 HA 0.090000 1.0080 0 16 | 10 BH 1 ALA C C 0.510000 12.0110 0 17 | 11 BH 1 ALA O O -0.510000 15.9990 0 18 | 12 BH 2 ALA N NH1 -0.470000 14.0070 0 19 | 13 BH 2 ALA HN H 0.310000 1.0080 0 20 | 14 BH 2 ALA CA CT1 0.070000 12.0110 0 21 | 15 BH 2 ALA HA HB 0.090000 1.0080 0 22 | 16 BH 2 ALA CB CT3 -0.270000 12.0110 0 23 | 17 BH 2 ALA HB1 HA 0.090000 1.0080 0 24 | 18 BH 2 ALA HB2 HA 0.090000 1.0080 0 25 | 19 BH 2 ALA HB3 HA 0.090000 1.0080 0 26 | 20 BH 2 ALA C C 0.510000 12.0110 0 27 | 21 BH 2 ALA O O -0.510000 15.9990 0 28 | 22 BH 3 ALA N NH1 -0.470000 14.0070 0 29 | 23 BH 3 ALA HN H 0.310000 1.0080 0 30 | 24 BH 3 ALA CA CT1 0.070000 12.0110 0 31 | 25 BH 3 ALA HA HB 0.090000 1.0080 0 32 | 26 BH 3 ALA CB CT3 -0.270000 12.0110 0 33 | 27 BH 3 ALA HB1 HA 0.090000 1.0080 0 34 | 28 BH 3 ALA HB2 HA 0.090000 1.0080 0 35 | 29 BH 3 ALA HB3 HA 0.090000 1.0080 0 36 | 30 BH 3 ALA C C 0.510000 12.0110 0 37 | 31 BH 3 ALA O O -0.510000 15.9990 0 38 | 32 BH 4 ALA N NH1 -0.470000 14.0070 0 39 | 33 BH 4 ALA HN H 0.310000 1.0080 0 40 | 34 BH 4 ALA CA CT1 0.070000 12.0110 0 41 | 35 BH 4 ALA HA HB 0.090000 1.0080 0 42 | 36 BH 4 ALA CB CT3 -0.270000 12.0110 0 43 | 37 BH 4 ALA HB1 HA 0.090000 1.0080 0 44 | 38 BH 4 ALA HB2 HA 0.090000 1.0080 0 45 | 39 BH 4 ALA HB3 HA 0.090000 1.0080 0 46 | 40 BH 4 ALA C C 0.510000 12.0110 0 47 | 41 BH 4 ALA O O -0.510000 15.9990 0 48 | 42 BH 5 ALA N NH1 -0.470000 14.0070 0 49 | 43 BH 5 ALA HN H 0.310000 1.0080 0 50 | 44 BH 5 ALA CA CT1 0.070000 12.0110 0 51 | 45 BH 5 ALA HA HB 0.090000 1.0080 0 52 | 46 BH 5 ALA CB CT3 -0.270000 12.0110 0 53 | 47 BH 5 ALA HB1 HA 0.090000 1.0080 0 54 | 48 BH 5 ALA HB2 HA 0.090000 1.0080 0 55 | 49 BH 5 ALA HB3 HA 0.090000 1.0080 0 56 | 50 BH 5 ALA C C 0.510000 12.0110 0 57 | 51 BH 5 ALA O O -0.510000 15.9990 0 58 | 52 BH 6 ALA N NH1 -0.470000 14.0070 0 59 | 53 BH 6 ALA HN H 0.310000 1.0080 0 60 | 54 BH 6 ALA CA CT1 0.070000 12.0110 0 61 | 55 BH 6 ALA HA HB 0.090000 1.0080 0 62 | 56 BH 6 ALA CB CT3 -0.270000 12.0110 0 63 | 57 BH 6 ALA HB1 HA 0.090000 1.0080 0 64 | 58 BH 6 ALA HB2 HA 0.090000 1.0080 0 65 | 59 BH 6 ALA HB3 HA 0.090000 1.0080 0 66 | 60 BH 6 ALA C C 0.510000 12.0110 0 67 | 61 BH 6 ALA O O -0.510000 15.9990 0 68 | 62 BH 7 ALA N NH1 -0.470000 14.0070 0 69 | 63 BH 7 ALA HN H 0.310000 1.0080 0 70 | 64 BH 7 ALA CA CT1 0.070000 12.0110 0 71 | 65 BH 7 ALA HA HB 0.090000 1.0080 0 72 | 66 BH 7 ALA CB CT3 -0.270000 12.0110 0 73 | 67 BH 7 ALA HB1 HA 0.090000 1.0080 0 74 | 68 BH 7 ALA HB2 HA 0.090000 1.0080 0 75 | 69 BH 7 ALA HB3 HA 0.090000 1.0080 0 76 | 70 BH 7 ALA C C 0.510000 12.0110 0 77 | 71 BH 7 ALA O O -0.510000 15.9990 0 78 | 72 BH 8 ALA N NH1 -0.470000 14.0070 0 79 | 73 BH 8 ALA HN H 0.310000 1.0080 0 80 | 74 BH 8 ALA CA CT1 0.070000 12.0110 0 81 | 75 BH 8 ALA HA HB 0.090000 1.0080 0 82 | 76 BH 8 ALA CB CT3 -0.270000 12.0110 0 83 | 77 BH 8 ALA HB1 HA 0.090000 1.0080 0 84 | 78 BH 8 ALA HB2 HA 0.090000 1.0080 0 85 | 79 BH 8 ALA HB3 HA 0.090000 1.0080 0 86 | 80 BH 8 ALA C C 0.510000 12.0110 0 87 | 81 BH 8 ALA O O -0.510000 15.9990 0 88 | 82 BH 9 ALA N NH1 -0.470000 14.0070 0 89 | 83 BH 9 ALA HN H 0.310000 1.0080 0 90 | 84 BH 9 ALA CA CT1 0.070000 12.0110 0 91 | 85 BH 9 ALA HA HB 0.090000 1.0080 0 92 | 86 BH 9 ALA CB CT3 -0.270000 12.0110 0 93 | 87 BH 9 ALA HB1 HA 0.090000 1.0080 0 94 | 88 BH 9 ALA HB2 HA 0.090000 1.0080 0 95 | 89 BH 9 ALA HB3 HA 0.090000 1.0080 0 96 | 90 BH 9 ALA C C 0.510000 12.0110 0 97 | 91 BH 9 ALA O O -0.510000 15.9990 0 98 | 92 BH 10 ALA C CC 0.550000 12.0110 0 99 | 93 BH 10 ALA O O -0.550000 15.9990 0 100 | 94 BH 10 ALA NT NH2 -0.620000 14.0070 0 101 | 95 BH 10 ALA HT1 H 0.320000 1.0080 0 102 | 96 BH 10 ALA HT2 H 0.300000 1.0080 0 103 | 97 BH 10 ALA N NH1 -0.470000 14.0070 0 104 | 98 BH 10 ALA HN H 0.310000 1.0080 0 105 | 99 BH 10 ALA CA CT1 0.070000 12.0110 0 106 | 100 BH 10 ALA HA HB 0.090000 1.0080 0 107 | 101 BH 10 ALA CB CT3 -0.270000 12.0110 0 108 | 102 BH 10 ALA HB1 HA 0.090000 1.0080 0 109 | 103 BH 10 ALA HB2 HA 0.090000 1.0080 0 110 | 104 BH 10 ALA HB3 HA 0.090000 1.0080 0 111 | 112 | 103 !NBOND: bonds 113 | 1 4 2 1 3 1 4 5 114 | 6 4 6 7 6 8 6 9 115 | 10 4 10 12 11 10 12 13 116 | 12 14 14 15 16 14 16 17 117 | 16 18 16 19 20 14 20 22 118 | 21 20 22 23 22 24 24 25 119 | 26 24 26 27 26 28 26 29 120 | 30 24 30 32 31 30 32 33 121 | 32 34 34 35 36 34 36 37 122 | 36 38 36 39 40 34 40 42 123 | 41 40 42 43 42 44 44 45 124 | 46 44 46 47 46 48 46 49 125 | 50 44 50 52 51 50 52 53 126 | 52 54 54 55 56 54 56 57 127 | 56 58 56 59 60 54 60 62 128 | 61 60 62 63 62 64 64 65 129 | 66 64 66 67 66 68 66 69 130 | 70 64 70 72 71 70 72 73 131 | 72 74 74 75 76 74 76 77 132 | 76 78 76 79 80 74 80 82 133 | 81 80 82 83 82 84 84 85 134 | 86 84 86 87 86 88 86 89 135 | 90 84 90 97 91 90 92 94 136 | 92 99 93 92 94 95 94 96 137 | 97 98 97 99 99 100 101 99 138 | 101 102 101 103 101 104 139 | 140 | 183 !NTHETA: angles 141 | 1 4 5 1 4 10 2 1 4 142 | 2 1 3 3 1 4 4 10 11 143 | 4 10 12 4 6 9 4 6 8 144 | 4 6 7 6 4 5 6 4 10 145 | 6 4 1 7 6 9 7 6 8 146 | 8 6 9 10 4 5 12 14 15 147 | 12 14 20 12 10 11 13 12 10 148 | 13 12 14 14 20 21 14 20 22 149 | 14 16 19 14 16 18 14 16 17 150 | 14 12 10 16 14 15 16 14 20 151 | 16 14 12 17 16 19 17 16 18 152 | 18 16 19 20 14 15 22 24 25 153 | 22 24 30 22 20 21 23 22 20 154 | 23 22 24 24 30 31 24 30 32 155 | 24 26 29 24 26 28 24 26 27 156 | 24 22 20 26 24 25 26 24 30 157 | 26 24 22 27 26 29 27 26 28 158 | 28 26 29 30 24 25 32 34 35 159 | 32 34 40 32 30 31 33 32 30 160 | 33 32 34 34 40 41 34 40 42 161 | 34 36 39 34 36 38 34 36 37 162 | 34 32 30 36 34 35 36 34 40 163 | 36 34 32 37 36 39 37 36 38 164 | 38 36 39 40 34 35 42 44 45 165 | 42 44 50 42 40 41 43 42 40 166 | 43 42 44 44 50 51 44 50 52 167 | 44 46 49 44 46 48 44 46 47 168 | 44 42 40 46 44 45 46 44 50 169 | 46 44 42 47 46 49 47 46 48 170 | 48 46 49 50 44 45 52 54 55 171 | 52 54 60 52 50 51 53 52 50 172 | 53 52 54 54 60 61 54 60 62 173 | 54 56 59 54 56 58 54 56 57 174 | 54 52 50 56 54 55 56 54 60 175 | 56 54 52 57 56 59 57 56 58 176 | 58 56 59 60 54 55 62 64 65 177 | 62 64 70 62 60 61 63 62 60 178 | 63 62 64 64 70 71 64 70 72 179 | 64 66 69 64 66 68 64 66 67 180 | 64 62 60 66 64 65 66 64 70 181 | 66 64 62 67 66 69 67 66 68 182 | 68 66 69 70 64 65 72 74 75 183 | 72 74 80 72 70 71 73 72 70 184 | 73 72 74 74 80 81 74 80 82 185 | 74 76 79 74 76 78 74 76 77 186 | 74 72 70 76 74 75 76 74 80 187 | 76 74 72 77 76 79 77 76 78 188 | 78 76 79 80 74 75 82 84 85 189 | 82 84 90 82 80 81 83 82 80 190 | 83 82 84 84 90 91 84 90 97 191 | 84 86 89 84 86 88 84 86 87 192 | 84 82 80 86 84 85 86 84 90 193 | 86 84 82 87 86 89 87 86 88 194 | 88 86 89 90 84 85 92 99 100 195 | 92 94 96 92 94 95 94 92 93 196 | 94 92 99 95 94 96 97 99 100 197 | 97 99 92 97 90 91 98 97 90 198 | 98 97 99 99 101 104 99 101 103 199 | 99 101 102 99 97 90 99 92 93 200 | 101 99 100 101 99 92 101 99 97 201 | 102 101 104 102 101 103 103 101 104 202 | 203 | 251 !NPHI: dihedrals 204 | 1 4 6 7 1 4 6 8 205 | 1 4 6 9 1 4 10 12 206 | 1 4 10 11 2 1 4 6 207 | 2 1 4 10 2 1 4 5 208 | 3 1 4 6 3 1 4 10 209 | 3 1 4 5 4 10 12 13 210 | 4 10 12 14 5 4 6 7 211 | 5 4 6 8 5 4 6 9 212 | 5 4 10 12 5 4 10 11 213 | 6 4 10 12 6 4 10 11 214 | 7 6 4 10 8 6 4 10 215 | 9 6 4 10 10 12 14 16 216 | 10 12 14 20 10 12 14 15 217 | 11 10 12 13 11 10 12 14 218 | 12 14 16 17 12 14 16 18 219 | 12 14 16 19 12 14 20 22 220 | 12 14 20 21 13 12 14 16 221 | 13 12 14 20 13 12 14 15 222 | 14 20 22 23 14 20 22 24 223 | 15 14 16 17 15 14 16 18 224 | 15 14 16 19 15 14 20 22 225 | 15 14 20 21 16 14 20 22 226 | 16 14 20 21 17 16 14 20 227 | 18 16 14 20 19 16 14 20 228 | 20 22 24 26 20 22 24 30 229 | 20 22 24 25 21 20 22 23 230 | 21 20 22 24 22 24 26 27 231 | 22 24 26 28 22 24 26 29 232 | 22 24 30 32 22 24 30 31 233 | 23 22 24 26 23 22 24 30 234 | 23 22 24 25 24 30 32 33 235 | 24 30 32 34 25 24 26 27 236 | 25 24 26 28 25 24 26 29 237 | 25 24 30 32 25 24 30 31 238 | 26 24 30 32 26 24 30 31 239 | 27 26 24 30 28 26 24 30 240 | 29 26 24 30 30 32 34 36 241 | 30 32 34 40 30 32 34 35 242 | 31 30 32 33 31 30 32 34 243 | 32 34 36 37 32 34 36 38 244 | 32 34 36 39 32 34 40 42 245 | 32 34 40 41 33 32 34 36 246 | 33 32 34 40 33 32 34 35 247 | 34 40 42 43 34 40 42 44 248 | 35 34 36 37 35 34 36 38 249 | 35 34 36 39 35 34 40 42 250 | 35 34 40 41 36 34 40 42 251 | 36 34 40 41 37 36 34 40 252 | 38 36 34 40 39 36 34 40 253 | 40 42 44 46 40 42 44 50 254 | 40 42 44 45 41 40 42 43 255 | 41 40 42 44 42 44 46 47 256 | 42 44 46 48 42 44 46 49 257 | 42 44 50 52 42 44 50 51 258 | 43 42 44 46 43 42 44 50 259 | 43 42 44 45 44 50 52 53 260 | 44 50 52 54 45 44 46 47 261 | 45 44 46 48 45 44 46 49 262 | 45 44 50 52 45 44 50 51 263 | 46 44 50 52 46 44 50 51 264 | 47 46 44 50 48 46 44 50 265 | 49 46 44 50 50 52 54 56 266 | 50 52 54 60 50 52 54 55 267 | 51 50 52 53 51 50 52 54 268 | 52 54 56 57 52 54 56 58 269 | 52 54 56 59 52 54 60 62 270 | 52 54 60 61 53 52 54 56 271 | 53 52 54 60 53 52 54 55 272 | 54 60 62 63 54 60 62 64 273 | 55 54 56 57 55 54 56 58 274 | 55 54 56 59 55 54 60 62 275 | 55 54 60 61 56 54 60 62 276 | 56 54 60 61 57 56 54 60 277 | 58 56 54 60 59 56 54 60 278 | 60 62 64 66 60 62 64 70 279 | 60 62 64 65 61 60 62 63 280 | 61 60 62 64 62 64 66 67 281 | 62 64 66 68 62 64 66 69 282 | 62 64 70 72 62 64 70 71 283 | 63 62 64 66 63 62 64 70 284 | 63 62 64 65 64 70 72 73 285 | 64 70 72 74 65 64 66 67 286 | 65 64 66 68 65 64 66 69 287 | 65 64 70 72 65 64 70 71 288 | 66 64 70 72 66 64 70 71 289 | 67 66 64 70 68 66 64 70 290 | 69 66 64 70 70 72 74 76 291 | 70 72 74 80 70 72 74 75 292 | 71 70 72 73 71 70 72 74 293 | 72 74 76 77 72 74 76 78 294 | 72 74 76 79 72 74 80 82 295 | 72 74 80 81 73 72 74 76 296 | 73 72 74 80 73 72 74 75 297 | 74 80 82 83 74 80 82 84 298 | 75 74 76 77 75 74 76 78 299 | 75 74 76 79 75 74 80 82 300 | 75 74 80 81 76 74 80 82 301 | 76 74 80 81 77 76 74 80 302 | 78 76 74 80 79 76 74 80 303 | 80 82 84 86 80 82 84 90 304 | 80 82 84 85 81 80 82 83 305 | 81 80 82 84 82 84 86 87 306 | 82 84 86 88 82 84 86 89 307 | 82 84 90 97 82 84 90 91 308 | 83 82 84 86 83 82 84 90 309 | 83 82 84 85 84 90 97 98 310 | 84 90 97 99 85 84 86 87 311 | 85 84 86 88 85 84 86 89 312 | 85 84 90 97 85 84 90 91 313 | 86 84 90 97 86 84 90 91 314 | 87 86 84 90 88 86 84 90 315 | 89 86 84 90 90 97 99 101 316 | 90 97 99 92 90 97 99 100 317 | 91 90 97 98 91 90 97 99 318 | 92 99 101 102 92 99 101 103 319 | 92 99 101 104 92 99 97 98 320 | 93 92 94 95 93 92 94 96 321 | 93 92 99 101 93 92 99 97 322 | 93 92 99 100 94 92 99 101 323 | 94 92 99 97 94 92 99 100 324 | 95 94 92 99 96 94 92 99 325 | 97 99 101 102 97 99 101 103 326 | 97 99 101 104 98 97 99 101 327 | 98 97 99 100 99 92 94 96 328 | 100 99 101 102 100 99 101 103 329 | 100 99 101 104 330 | 331 | 22 !NIMPHI: impropers 332 | 10 4 12 11 12 10 14 13 333 | 20 14 22 21 22 20 24 23 334 | 30 24 32 31 32 30 34 33 335 | 40 34 42 41 42 40 44 43 336 | 50 44 52 51 52 50 54 53 337 | 60 54 62 61 62 60 64 63 338 | 70 64 72 71 72 70 74 73 339 | 80 74 82 81 82 80 84 83 340 | 90 84 97 91 92 94 99 93 341 | 92 99 94 93 94 92 95 96 342 | 94 92 96 95 97 90 99 98 343 | 344 | 0 !NDON: donors 345 | 346 | 347 | 0 !NACC: acceptors 348 | 349 | 350 | 0 !NNB 351 | 352 | 0 0 0 0 0 0 0 0 353 | 0 0 0 0 0 0 0 0 354 | 0 0 0 0 0 0 0 0 355 | 0 0 0 0 0 0 0 0 356 | 0 0 0 0 0 0 0 0 357 | 0 0 0 0 0 0 0 0 358 | 0 0 0 0 0 0 0 0 359 | 0 0 0 0 0 0 0 0 360 | 0 0 0 0 0 0 0 0 361 | 0 0 0 0 0 0 0 0 362 | 0 0 0 0 0 0 0 0 363 | 0 0 0 0 0 0 0 0 364 | 0 0 0 0 0 0 0 0 365 | 366 | 367 | 1 0 !NGRP 368 | 0 0 0 369 | 370 | -------------------------------------------------------------------------------- /NAMD_Colvars/eABF/Distance.in: -------------------------------------------------------------------------------- 1 | colvarsTrajFrequency 1000 2 | colvarsRestartFrequency 50000 3 | 4 | colvar { 5 | name AtomDistance 6 | 7 | width 0.1 8 | 9 | lowerboundary 12.0 10 | upperboundary 32.0 11 | 12 | lowerwallconstant 10.0 13 | upperwallconstant 10.0 14 | 15 | extendedLagrangian on 16 | extendedFluctuation 0.1 17 | 18 | distance { 19 | group1 { 20 | atomnumbers { 10 } 21 | } 22 | group2 { 23 | atomnumbers { 92 } 24 | } 25 | } 26 | } 27 | 28 | 29 | abf { 30 | colvars AtomDistance 31 | fullSamples 500 32 | } 33 | -------------------------------------------------------------------------------- /NAMD_Colvars/eABF/abf.conf: -------------------------------------------------------------------------------- 1 | ################################################## 2 | ################################################## 3 | # 4 | # ABF calculation 5 | # 6 | # Deca-alanine 7 | # 8 | ################################################## 9 | ################################################## 10 | 11 | 12 | ################################################## 13 | # MD SECTION 14 | ################################################## 15 | 16 | 17 | # NUMBER OF MD-STEPS 18 | 19 | numsteps 20000000 20 | 21 | 22 | # TOPOLOGY 23 | 24 | structure deca-ala.psf 25 | 26 | 27 | # FORCE FIELD 28 | 29 | parameters par_all22_prot.inp 30 | paraTypeCharmm on 31 | 32 | 33 | # 1-4 TERMs 34 | 35 | exclude scaled1-4 36 | 1-4scaling 1.0 37 | 38 | 39 | # INPUT FILES 40 | 41 | coordinates deca-ala.pdb 42 | 43 | temperature 300.0 44 | 45 | # OUTPUT FILES 46 | 47 | outputname output/abf 48 | 49 | 50 | # FREQUENCY FOR DUMPING OUTPUT DATA 51 | 52 | outputenergies 1000 53 | outputtiming 1000 54 | outputpressure 1000 55 | restartfreq 1000 56 | XSTFreq 1000 57 | dcdFreq 1000 58 | 59 | 60 | # CUT-OFFs 61 | 62 | hgroupcutoff 2.8 63 | switching on 64 | switchdist 10.0 65 | cutoff 12.0 66 | pairlistdist 14.0 67 | 68 | 69 | # CONSTANT-T 70 | 71 | langevin on 72 | langevintemp 300.0 73 | langevindamping 1.0 74 | 75 | 76 | # MULTIPLE TIME-STEP PROPAGATOR 77 | 78 | timestep 0.5 79 | 80 | 81 | # SHAKE/RATTLE 82 | 83 | rigidbonds none 84 | 85 | 86 | # PARALLELISM 87 | 88 | stepspercycle 16 89 | splitpatch hydrogen 90 | margin 2.0 91 | 92 | 93 | # ABF SECTION 94 | 95 | colvars on 96 | colvarsConfig Distance.in 97 | -------------------------------------------------------------------------------- /NAMD_Colvars/eABF/deca-ala.pdb: -------------------------------------------------------------------------------- 1 | REMARK FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 50000 2 | ATOM 1 N ALA B 1 0.113 -2.288 -1.254 1.00 0.00 BH 3 | ATOM 2 HT2 ALA B 1 -0.779 -1.974 -1.687 1.00 0.00 BH 4 | ATOM 3 HT3 ALA B 1 0.803 -2.829 -1.813 1.00 0.00 BH 5 | ATOM 4 CA ALA B 1 0.767 -1.116 -0.506 1.00 0.00 BH 6 | ATOM 5 HA ALA B 1 1.714 -1.559 -0.234 1.00 0.00 BH 7 | ATOM 6 CB ALA B 1 0.790 0.006 -1.515 1.00 0.00 BH 8 | ATOM 7 HB1 ALA B 1 1.247 0.922 -1.085 1.00 0.00 BH 9 | ATOM 8 HB2 ALA B 1 1.323 -0.411 -2.396 1.00 0.00 BH 10 | ATOM 9 HB3 ALA B 1 -0.176 0.421 -1.873 1.00 0.00 BH 11 | ATOM 10 C ALA B 1 -0.064 -0.634 0.728 1.00 0.00 BH 12 | ATOM 11 O ALA B 1 -1.283 -0.502 0.585 1.00 0.00 BH 13 | ATOM 12 N ALA B 2 0.567 -0.384 1.892 1.00 0.00 BH 14 | ATOM 13 HN ALA B 2 1.558 -0.447 1.979 1.00 0.00 BH 15 | ATOM 14 CA ALA B 2 -0.136 -0.308 3.124 1.00 0.00 BH 16 | ATOM 15 HA ALA B 2 -0.582 -1.269 3.333 1.00 0.00 BH 17 | ATOM 16 CB ALA B 2 0.894 -0.058 4.221 1.00 0.00 BH 18 | ATOM 17 HB1 ALA B 2 0.586 0.170 5.264 1.00 0.00 BH 19 | ATOM 18 HB2 ALA B 2 1.386 -1.043 4.368 1.00 0.00 BH 20 | ATOM 19 HB3 ALA B 2 1.572 0.761 3.896 1.00 0.00 BH 21 | ATOM 20 C ALA B 2 -1.193 0.854 3.162 1.00 0.00 BH 22 | ATOM 21 O ALA B 2 -2.372 0.602 3.566 1.00 0.00 BH 23 | ATOM 22 N ALA B 3 -0.856 2.141 2.875 1.00 0.00 BH 24 | ATOM 23 HN ALA B 3 0.082 2.422 2.689 1.00 0.00 BH 25 | ATOM 24 CA ALA B 3 -1.733 3.280 2.950 1.00 0.00 BH 26 | ATOM 25 HA ALA B 3 -1.997 3.414 3.989 1.00 0.00 BH 27 | ATOM 26 CB ALA B 3 -0.919 4.499 2.477 1.00 0.00 BH 28 | ATOM 27 HB1 ALA B 3 -0.655 4.413 1.401 1.00 0.00 BH 29 | ATOM 28 HB2 ALA B 3 -1.373 5.496 2.661 1.00 0.00 BH 30 | ATOM 29 HB3 ALA B 3 0.046 4.517 3.027 1.00 0.00 BH 31 | ATOM 30 C ALA B 3 -3.066 3.199 2.243 1.00 0.00 BH 32 | ATOM 31 O ALA B 3 -4.119 3.466 2.841 1.00 0.00 BH 33 | ATOM 32 N ALA B 4 -3.071 2.558 1.079 1.00 0.00 BH 34 | ATOM 33 HN ALA B 4 -2.166 2.271 0.776 1.00 0.00 BH 35 | ATOM 34 CA ALA B 4 -4.295 2.275 0.353 1.00 0.00 BH 36 | ATOM 35 HA ALA B 4 -4.896 3.161 0.210 1.00 0.00 BH 37 | ATOM 36 CB ALA B 4 -3.971 1.919 -1.163 1.00 0.00 BH 38 | ATOM 37 HB1 ALA B 4 -3.481 2.802 -1.626 1.00 0.00 BH 39 | ATOM 38 HB2 ALA B 4 -3.239 1.084 -1.214 1.00 0.00 BH 40 | ATOM 39 HB3 ALA B 4 -4.905 1.551 -1.638 1.00 0.00 BH 41 | ATOM 40 C ALA B 4 -5.138 1.148 1.014 1.00 0.00 BH 42 | ATOM 41 O ALA B 4 -6.290 1.290 1.505 1.00 0.00 BH 43 | ATOM 42 N ALA B 5 -4.485 -0.069 0.981 1.00 0.00 BH 44 | ATOM 43 HN ALA B 5 -3.535 -0.144 0.687 1.00 0.00 BH 45 | ATOM 44 CA ALA B 5 -4.953 -1.327 1.563 1.00 0.00 BH 46 | ATOM 45 HA ALA B 5 -5.600 -1.791 0.833 1.00 0.00 BH 47 | ATOM 46 CB ALA B 5 -3.792 -2.416 1.640 1.00 0.00 BH 48 | ATOM 47 HB1 ALA B 5 -3.238 -2.513 0.682 1.00 0.00 BH 49 | ATOM 48 HB2 ALA B 5 -3.051 -2.249 2.451 1.00 0.00 BH 50 | ATOM 49 HB3 ALA B 5 -4.151 -3.455 1.805 1.00 0.00 BH 51 | ATOM 50 C ALA B 5 -5.728 -1.269 2.853 1.00 0.00 BH 52 | ATOM 51 O ALA B 5 -6.821 -1.826 3.026 1.00 0.00 BH 53 | ATOM 52 N ALA B 6 -5.092 -0.721 3.920 1.00 0.00 BH 54 | ATOM 53 HN ALA B 6 -4.250 -0.199 3.808 1.00 0.00 BH 55 | ATOM 54 CA ALA B 6 -5.756 -0.450 5.212 1.00 0.00 BH 56 | ATOM 55 HA ALA B 6 -6.319 -1.344 5.435 1.00 0.00 BH 57 | ATOM 56 CB ALA B 6 -4.701 -0.089 6.243 1.00 0.00 BH 58 | ATOM 57 HB1 ALA B 6 -4.174 0.836 5.923 1.00 0.00 BH 59 | ATOM 58 HB2 ALA B 6 -5.122 -0.006 7.268 1.00 0.00 BH 60 | ATOM 59 HB3 ALA B 6 -4.066 -0.993 6.365 1.00 0.00 BH 61 | ATOM 60 C ALA B 6 -6.839 0.547 5.134 1.00 0.00 BH 62 | ATOM 61 O ALA B 6 -7.796 0.344 5.789 1.00 0.00 BH 63 | ATOM 62 N ALA B 7 -6.709 1.632 4.377 1.00 0.00 BH 64 | ATOM 63 HN ALA B 7 -5.900 1.830 3.830 1.00 0.00 BH 65 | ATOM 64 CA ALA B 7 -7.707 2.606 4.337 1.00 0.00 BH 66 | ATOM 65 HA ALA B 7 -8.028 2.824 5.345 1.00 0.00 BH 67 | ATOM 66 CB ALA B 7 -6.920 3.781 3.934 1.00 0.00 BH 68 | ATOM 67 HB1 ALA B 7 -6.703 3.722 2.846 1.00 0.00 BH 69 | ATOM 68 HB2 ALA B 7 -7.445 4.746 4.096 1.00 0.00 BH 70 | ATOM 69 HB3 ALA B 7 -5.940 3.795 4.458 1.00 0.00 BH 71 | ATOM 70 C ALA B 7 -8.912 2.354 3.463 1.00 0.00 BH 72 | ATOM 71 O ALA B 7 -9.974 2.853 3.663 1.00 0.00 BH 73 | ATOM 72 N ALA B 8 -8.864 1.404 2.514 1.00 0.00 BH 74 | ATOM 73 HN ALA B 8 -7.932 1.244 2.200 1.00 0.00 BH 75 | ATOM 74 CA ALA B 8 -10.008 0.910 1.816 1.00 0.00 BH 76 | ATOM 75 HA ALA B 8 -10.785 1.635 1.621 1.00 0.00 BH 77 | ATOM 76 CB ALA B 8 -9.572 0.291 0.457 1.00 0.00 BH 78 | ATOM 77 HB1 ALA B 8 -10.397 -0.326 0.040 1.00 0.00 BH 79 | ATOM 78 HB2 ALA B 8 -9.311 1.110 -0.247 1.00 0.00 BH 80 | ATOM 79 HB3 ALA B 8 -8.793 -0.479 0.643 1.00 0.00 BH 81 | ATOM 80 C ALA B 8 -10.663 -0.166 2.707 1.00 0.00 BH 82 | ATOM 81 O ALA B 8 -11.882 -0.432 2.666 1.00 0.00 BH 83 | ATOM 82 N ALA B 9 -9.886 -0.789 3.580 1.00 0.00 BH 84 | ATOM 83 HN ALA B 9 -8.904 -0.621 3.609 1.00 0.00 BH 85 | ATOM 84 CA ALA B 9 -10.404 -1.774 4.539 1.00 0.00 BH 86 | ATOM 85 HA ALA B 9 -10.996 -2.532 4.049 1.00 0.00 BH 87 | ATOM 86 CB ALA B 9 -9.238 -2.543 5.191 1.00 0.00 BH 88 | ATOM 87 HB1 ALA B 9 -8.806 -3.097 4.331 1.00 0.00 BH 89 | ATOM 88 HB2 ALA B 9 -8.467 -1.819 5.532 1.00 0.00 BH 90 | ATOM 89 HB3 ALA B 9 -9.463 -3.262 6.007 1.00 0.00 BH 91 | ATOM 90 C ALA B 9 -11.212 -1.063 5.618 1.00 0.00 BH 92 | ATOM 91 O ALA B 9 -12.370 -1.417 5.769 1.00 0.00 BH 93 | ATOM 92 C ALA B 10 -11.957 1.980 7.072 1.00 0.00 BH 94 | ATOM 93 O ALA B 10 -11.964 3.008 7.760 1.00 0.00 BH 95 | ATOM 94 NT ALA B 10 -12.813 1.968 5.971 1.00 0.00 BH 96 | ATOM 95 HT1 ALA B 10 -13.399 2.748 5.755 1.00 0.00 BH 97 | ATOM 96 HT2 ALA B 10 -12.618 1.237 5.316 1.00 0.00 BH 98 | ATOM 97 N ALA B 10 -10.690 0.020 6.213 1.00 0.00 BH 99 | ATOM 98 HN ALA B 10 -9.720 0.133 6.012 1.00 0.00 BH 100 | ATOM 99 CA ALA B 10 -11.166 0.664 7.402 1.00 0.00 BH 101 | ATOM 100 HA ALA B 10 -11.936 0.058 7.856 1.00 0.00 BH 102 | ATOM 101 CB ALA B 10 -10.058 0.920 8.404 1.00 0.00 BH 103 | ATOM 102 HB1 ALA B 10 -9.202 1.387 7.871 1.00 0.00 BH 104 | ATOM 103 HB2 ALA B 10 -10.427 1.550 9.242 1.00 0.00 BH 105 | ATOM 104 HB3 ALA B 10 -9.603 -0.048 8.702 1.00 0.00 BH 106 | END 107 | -------------------------------------------------------------------------------- /NAMD_Colvars/eABF/deca-ala.psf: -------------------------------------------------------------------------------- 1 | PSF 2 | 3 | 1 !NTITLE 4 | REMARKS original generated structure x-plor psf file 5 | 6 | 104 !NATOM 7 | 1 BH 1 ALA N NH3 -0.620000 14.0070 0 8 | 2 BH 1 ALA HT2 HC 0.310000 1.0080 0 9 | 3 BH 1 ALA HT3 HC 0.310000 1.0080 0 10 | 4 BH 1 ALA CA CT1 -0.100000 12.0110 0 11 | 5 BH 1 ALA HA HB 0.100000 1.0080 0 12 | 6 BH 1 ALA CB CT3 -0.270000 12.0110 0 13 | 7 BH 1 ALA HB1 HA 0.090000 1.0080 0 14 | 8 BH 1 ALA HB2 HA 0.090000 1.0080 0 15 | 9 BH 1 ALA HB3 HA 0.090000 1.0080 0 16 | 10 BH 1 ALA C C 0.510000 12.0110 0 17 | 11 BH 1 ALA O O -0.510000 15.9990 0 18 | 12 BH 2 ALA N NH1 -0.470000 14.0070 0 19 | 13 BH 2 ALA HN H 0.310000 1.0080 0 20 | 14 BH 2 ALA CA CT1 0.070000 12.0110 0 21 | 15 BH 2 ALA HA HB 0.090000 1.0080 0 22 | 16 BH 2 ALA CB CT3 -0.270000 12.0110 0 23 | 17 BH 2 ALA HB1 HA 0.090000 1.0080 0 24 | 18 BH 2 ALA HB2 HA 0.090000 1.0080 0 25 | 19 BH 2 ALA HB3 HA 0.090000 1.0080 0 26 | 20 BH 2 ALA C C 0.510000 12.0110 0 27 | 21 BH 2 ALA O O -0.510000 15.9990 0 28 | 22 BH 3 ALA N NH1 -0.470000 14.0070 0 29 | 23 BH 3 ALA HN H 0.310000 1.0080 0 30 | 24 BH 3 ALA CA CT1 0.070000 12.0110 0 31 | 25 BH 3 ALA HA HB 0.090000 1.0080 0 32 | 26 BH 3 ALA CB CT3 -0.270000 12.0110 0 33 | 27 BH 3 ALA HB1 HA 0.090000 1.0080 0 34 | 28 BH 3 ALA HB2 HA 0.090000 1.0080 0 35 | 29 BH 3 ALA HB3 HA 0.090000 1.0080 0 36 | 30 BH 3 ALA C C 0.510000 12.0110 0 37 | 31 BH 3 ALA O O -0.510000 15.9990 0 38 | 32 BH 4 ALA N NH1 -0.470000 14.0070 0 39 | 33 BH 4 ALA HN H 0.310000 1.0080 0 40 | 34 BH 4 ALA CA CT1 0.070000 12.0110 0 41 | 35 BH 4 ALA HA HB 0.090000 1.0080 0 42 | 36 BH 4 ALA CB CT3 -0.270000 12.0110 0 43 | 37 BH 4 ALA HB1 HA 0.090000 1.0080 0 44 | 38 BH 4 ALA HB2 HA 0.090000 1.0080 0 45 | 39 BH 4 ALA HB3 HA 0.090000 1.0080 0 46 | 40 BH 4 ALA C C 0.510000 12.0110 0 47 | 41 BH 4 ALA O O -0.510000 15.9990 0 48 | 42 BH 5 ALA N NH1 -0.470000 14.0070 0 49 | 43 BH 5 ALA HN H 0.310000 1.0080 0 50 | 44 BH 5 ALA CA CT1 0.070000 12.0110 0 51 | 45 BH 5 ALA HA HB 0.090000 1.0080 0 52 | 46 BH 5 ALA CB CT3 -0.270000 12.0110 0 53 | 47 BH 5 ALA HB1 HA 0.090000 1.0080 0 54 | 48 BH 5 ALA HB2 HA 0.090000 1.0080 0 55 | 49 BH 5 ALA HB3 HA 0.090000 1.0080 0 56 | 50 BH 5 ALA C C 0.510000 12.0110 0 57 | 51 BH 5 ALA O O -0.510000 15.9990 0 58 | 52 BH 6 ALA N NH1 -0.470000 14.0070 0 59 | 53 BH 6 ALA HN H 0.310000 1.0080 0 60 | 54 BH 6 ALA CA CT1 0.070000 12.0110 0 61 | 55 BH 6 ALA HA HB 0.090000 1.0080 0 62 | 56 BH 6 ALA CB CT3 -0.270000 12.0110 0 63 | 57 BH 6 ALA HB1 HA 0.090000 1.0080 0 64 | 58 BH 6 ALA HB2 HA 0.090000 1.0080 0 65 | 59 BH 6 ALA HB3 HA 0.090000 1.0080 0 66 | 60 BH 6 ALA C C 0.510000 12.0110 0 67 | 61 BH 6 ALA O O -0.510000 15.9990 0 68 | 62 BH 7 ALA N NH1 -0.470000 14.0070 0 69 | 63 BH 7 ALA HN H 0.310000 1.0080 0 70 | 64 BH 7 ALA CA CT1 0.070000 12.0110 0 71 | 65 BH 7 ALA HA HB 0.090000 1.0080 0 72 | 66 BH 7 ALA CB CT3 -0.270000 12.0110 0 73 | 67 BH 7 ALA HB1 HA 0.090000 1.0080 0 74 | 68 BH 7 ALA HB2 HA 0.090000 1.0080 0 75 | 69 BH 7 ALA HB3 HA 0.090000 1.0080 0 76 | 70 BH 7 ALA C C 0.510000 12.0110 0 77 | 71 BH 7 ALA O O -0.510000 15.9990 0 78 | 72 BH 8 ALA N NH1 -0.470000 14.0070 0 79 | 73 BH 8 ALA HN H 0.310000 1.0080 0 80 | 74 BH 8 ALA CA CT1 0.070000 12.0110 0 81 | 75 BH 8 ALA HA HB 0.090000 1.0080 0 82 | 76 BH 8 ALA CB CT3 -0.270000 12.0110 0 83 | 77 BH 8 ALA HB1 HA 0.090000 1.0080 0 84 | 78 BH 8 ALA HB2 HA 0.090000 1.0080 0 85 | 79 BH 8 ALA HB3 HA 0.090000 1.0080 0 86 | 80 BH 8 ALA C C 0.510000 12.0110 0 87 | 81 BH 8 ALA O O -0.510000 15.9990 0 88 | 82 BH 9 ALA N NH1 -0.470000 14.0070 0 89 | 83 BH 9 ALA HN H 0.310000 1.0080 0 90 | 84 BH 9 ALA CA CT1 0.070000 12.0110 0 91 | 85 BH 9 ALA HA HB 0.090000 1.0080 0 92 | 86 BH 9 ALA CB CT3 -0.270000 12.0110 0 93 | 87 BH 9 ALA HB1 HA 0.090000 1.0080 0 94 | 88 BH 9 ALA HB2 HA 0.090000 1.0080 0 95 | 89 BH 9 ALA HB3 HA 0.090000 1.0080 0 96 | 90 BH 9 ALA C C 0.510000 12.0110 0 97 | 91 BH 9 ALA O O -0.510000 15.9990 0 98 | 92 BH 10 ALA C CC 0.550000 12.0110 0 99 | 93 BH 10 ALA O O -0.550000 15.9990 0 100 | 94 BH 10 ALA NT NH2 -0.620000 14.0070 0 101 | 95 BH 10 ALA HT1 H 0.320000 1.0080 0 102 | 96 BH 10 ALA HT2 H 0.300000 1.0080 0 103 | 97 BH 10 ALA N NH1 -0.470000 14.0070 0 104 | 98 BH 10 ALA HN H 0.310000 1.0080 0 105 | 99 BH 10 ALA CA CT1 0.070000 12.0110 0 106 | 100 BH 10 ALA HA HB 0.090000 1.0080 0 107 | 101 BH 10 ALA CB CT3 -0.270000 12.0110 0 108 | 102 BH 10 ALA HB1 HA 0.090000 1.0080 0 109 | 103 BH 10 ALA HB2 HA 0.090000 1.0080 0 110 | 104 BH 10 ALA HB3 HA 0.090000 1.0080 0 111 | 112 | 103 !NBOND: bonds 113 | 1 4 2 1 3 1 4 5 114 | 6 4 6 7 6 8 6 9 115 | 10 4 10 12 11 10 12 13 116 | 12 14 14 15 16 14 16 17 117 | 16 18 16 19 20 14 20 22 118 | 21 20 22 23 22 24 24 25 119 | 26 24 26 27 26 28 26 29 120 | 30 24 30 32 31 30 32 33 121 | 32 34 34 35 36 34 36 37 122 | 36 38 36 39 40 34 40 42 123 | 41 40 42 43 42 44 44 45 124 | 46 44 46 47 46 48 46 49 125 | 50 44 50 52 51 50 52 53 126 | 52 54 54 55 56 54 56 57 127 | 56 58 56 59 60 54 60 62 128 | 61 60 62 63 62 64 64 65 129 | 66 64 66 67 66 68 66 69 130 | 70 64 70 72 71 70 72 73 131 | 72 74 74 75 76 74 76 77 132 | 76 78 76 79 80 74 80 82 133 | 81 80 82 83 82 84 84 85 134 | 86 84 86 87 86 88 86 89 135 | 90 84 90 97 91 90 92 94 136 | 92 99 93 92 94 95 94 96 137 | 97 98 97 99 99 100 101 99 138 | 101 102 101 103 101 104 139 | 140 | 183 !NTHETA: angles 141 | 1 4 5 1 4 10 2 1 4 142 | 2 1 3 3 1 4 4 10 11 143 | 4 10 12 4 6 9 4 6 8 144 | 4 6 7 6 4 5 6 4 10 145 | 6 4 1 7 6 9 7 6 8 146 | 8 6 9 10 4 5 12 14 15 147 | 12 14 20 12 10 11 13 12 10 148 | 13 12 14 14 20 21 14 20 22 149 | 14 16 19 14 16 18 14 16 17 150 | 14 12 10 16 14 15 16 14 20 151 | 16 14 12 17 16 19 17 16 18 152 | 18 16 19 20 14 15 22 24 25 153 | 22 24 30 22 20 21 23 22 20 154 | 23 22 24 24 30 31 24 30 32 155 | 24 26 29 24 26 28 24 26 27 156 | 24 22 20 26 24 25 26 24 30 157 | 26 24 22 27 26 29 27 26 28 158 | 28 26 29 30 24 25 32 34 35 159 | 32 34 40 32 30 31 33 32 30 160 | 33 32 34 34 40 41 34 40 42 161 | 34 36 39 34 36 38 34 36 37 162 | 34 32 30 36 34 35 36 34 40 163 | 36 34 32 37 36 39 37 36 38 164 | 38 36 39 40 34 35 42 44 45 165 | 42 44 50 42 40 41 43 42 40 166 | 43 42 44 44 50 51 44 50 52 167 | 44 46 49 44 46 48 44 46 47 168 | 44 42 40 46 44 45 46 44 50 169 | 46 44 42 47 46 49 47 46 48 170 | 48 46 49 50 44 45 52 54 55 171 | 52 54 60 52 50 51 53 52 50 172 | 53 52 54 54 60 61 54 60 62 173 | 54 56 59 54 56 58 54 56 57 174 | 54 52 50 56 54 55 56 54 60 175 | 56 54 52 57 56 59 57 56 58 176 | 58 56 59 60 54 55 62 64 65 177 | 62 64 70 62 60 61 63 62 60 178 | 63 62 64 64 70 71 64 70 72 179 | 64 66 69 64 66 68 64 66 67 180 | 64 62 60 66 64 65 66 64 70 181 | 66 64 62 67 66 69 67 66 68 182 | 68 66 69 70 64 65 72 74 75 183 | 72 74 80 72 70 71 73 72 70 184 | 73 72 74 74 80 81 74 80 82 185 | 74 76 79 74 76 78 74 76 77 186 | 74 72 70 76 74 75 76 74 80 187 | 76 74 72 77 76 79 77 76 78 188 | 78 76 79 80 74 75 82 84 85 189 | 82 84 90 82 80 81 83 82 80 190 | 83 82 84 84 90 91 84 90 97 191 | 84 86 89 84 86 88 84 86 87 192 | 84 82 80 86 84 85 86 84 90 193 | 86 84 82 87 86 89 87 86 88 194 | 88 86 89 90 84 85 92 99 100 195 | 92 94 96 92 94 95 94 92 93 196 | 94 92 99 95 94 96 97 99 100 197 | 97 99 92 97 90 91 98 97 90 198 | 98 97 99 99 101 104 99 101 103 199 | 99 101 102 99 97 90 99 92 93 200 | 101 99 100 101 99 92 101 99 97 201 | 102 101 104 102 101 103 103 101 104 202 | 203 | 251 !NPHI: dihedrals 204 | 1 4 6 7 1 4 6 8 205 | 1 4 6 9 1 4 10 12 206 | 1 4 10 11 2 1 4 6 207 | 2 1 4 10 2 1 4 5 208 | 3 1 4 6 3 1 4 10 209 | 3 1 4 5 4 10 12 13 210 | 4 10 12 14 5 4 6 7 211 | 5 4 6 8 5 4 6 9 212 | 5 4 10 12 5 4 10 11 213 | 6 4 10 12 6 4 10 11 214 | 7 6 4 10 8 6 4 10 215 | 9 6 4 10 10 12 14 16 216 | 10 12 14 20 10 12 14 15 217 | 11 10 12 13 11 10 12 14 218 | 12 14 16 17 12 14 16 18 219 | 12 14 16 19 12 14 20 22 220 | 12 14 20 21 13 12 14 16 221 | 13 12 14 20 13 12 14 15 222 | 14 20 22 23 14 20 22 24 223 | 15 14 16 17 15 14 16 18 224 | 15 14 16 19 15 14 20 22 225 | 15 14 20 21 16 14 20 22 226 | 16 14 20 21 17 16 14 20 227 | 18 16 14 20 19 16 14 20 228 | 20 22 24 26 20 22 24 30 229 | 20 22 24 25 21 20 22 23 230 | 21 20 22 24 22 24 26 27 231 | 22 24 26 28 22 24 26 29 232 | 22 24 30 32 22 24 30 31 233 | 23 22 24 26 23 22 24 30 234 | 23 22 24 25 24 30 32 33 235 | 24 30 32 34 25 24 26 27 236 | 25 24 26 28 25 24 26 29 237 | 25 24 30 32 25 24 30 31 238 | 26 24 30 32 26 24 30 31 239 | 27 26 24 30 28 26 24 30 240 | 29 26 24 30 30 32 34 36 241 | 30 32 34 40 30 32 34 35 242 | 31 30 32 33 31 30 32 34 243 | 32 34 36 37 32 34 36 38 244 | 32 34 36 39 32 34 40 42 245 | 32 34 40 41 33 32 34 36 246 | 33 32 34 40 33 32 34 35 247 | 34 40 42 43 34 40 42 44 248 | 35 34 36 37 35 34 36 38 249 | 35 34 36 39 35 34 40 42 250 | 35 34 40 41 36 34 40 42 251 | 36 34 40 41 37 36 34 40 252 | 38 36 34 40 39 36 34 40 253 | 40 42 44 46 40 42 44 50 254 | 40 42 44 45 41 40 42 43 255 | 41 40 42 44 42 44 46 47 256 | 42 44 46 48 42 44 46 49 257 | 42 44 50 52 42 44 50 51 258 | 43 42 44 46 43 42 44 50 259 | 43 42 44 45 44 50 52 53 260 | 44 50 52 54 45 44 46 47 261 | 45 44 46 48 45 44 46 49 262 | 45 44 50 52 45 44 50 51 263 | 46 44 50 52 46 44 50 51 264 | 47 46 44 50 48 46 44 50 265 | 49 46 44 50 50 52 54 56 266 | 50 52 54 60 50 52 54 55 267 | 51 50 52 53 51 50 52 54 268 | 52 54 56 57 52 54 56 58 269 | 52 54 56 59 52 54 60 62 270 | 52 54 60 61 53 52 54 56 271 | 53 52 54 60 53 52 54 55 272 | 54 60 62 63 54 60 62 64 273 | 55 54 56 57 55 54 56 58 274 | 55 54 56 59 55 54 60 62 275 | 55 54 60 61 56 54 60 62 276 | 56 54 60 61 57 56 54 60 277 | 58 56 54 60 59 56 54 60 278 | 60 62 64 66 60 62 64 70 279 | 60 62 64 65 61 60 62 63 280 | 61 60 62 64 62 64 66 67 281 | 62 64 66 68 62 64 66 69 282 | 62 64 70 72 62 64 70 71 283 | 63 62 64 66 63 62 64 70 284 | 63 62 64 65 64 70 72 73 285 | 64 70 72 74 65 64 66 67 286 | 65 64 66 68 65 64 66 69 287 | 65 64 70 72 65 64 70 71 288 | 66 64 70 72 66 64 70 71 289 | 67 66 64 70 68 66 64 70 290 | 69 66 64 70 70 72 74 76 291 | 70 72 74 80 70 72 74 75 292 | 71 70 72 73 71 70 72 74 293 | 72 74 76 77 72 74 76 78 294 | 72 74 76 79 72 74 80 82 295 | 72 74 80 81 73 72 74 76 296 | 73 72 74 80 73 72 74 75 297 | 74 80 82 83 74 80 82 84 298 | 75 74 76 77 75 74 76 78 299 | 75 74 76 79 75 74 80 82 300 | 75 74 80 81 76 74 80 82 301 | 76 74 80 81 77 76 74 80 302 | 78 76 74 80 79 76 74 80 303 | 80 82 84 86 80 82 84 90 304 | 80 82 84 85 81 80 82 83 305 | 81 80 82 84 82 84 86 87 306 | 82 84 86 88 82 84 86 89 307 | 82 84 90 97 82 84 90 91 308 | 83 82 84 86 83 82 84 90 309 | 83 82 84 85 84 90 97 98 310 | 84 90 97 99 85 84 86 87 311 | 85 84 86 88 85 84 86 89 312 | 85 84 90 97 85 84 90 91 313 | 86 84 90 97 86 84 90 91 314 | 87 86 84 90 88 86 84 90 315 | 89 86 84 90 90 97 99 101 316 | 90 97 99 92 90 97 99 100 317 | 91 90 97 98 91 90 97 99 318 | 92 99 101 102 92 99 101 103 319 | 92 99 101 104 92 99 97 98 320 | 93 92 94 95 93 92 94 96 321 | 93 92 99 101 93 92 99 97 322 | 93 92 99 100 94 92 99 101 323 | 94 92 99 97 94 92 99 100 324 | 95 94 92 99 96 94 92 99 325 | 97 99 101 102 97 99 101 103 326 | 97 99 101 104 98 97 99 101 327 | 98 97 99 100 99 92 94 96 328 | 100 99 101 102 100 99 101 103 329 | 100 99 101 104 330 | 331 | 22 !NIMPHI: impropers 332 | 10 4 12 11 12 10 14 13 333 | 20 14 22 21 22 20 24 23 334 | 30 24 32 31 32 30 34 33 335 | 40 34 42 41 42 40 44 43 336 | 50 44 52 51 52 50 54 53 337 | 60 54 62 61 62 60 64 63 338 | 70 64 72 71 72 70 74 73 339 | 80 74 82 81 82 80 84 83 340 | 90 84 97 91 92 94 99 93 341 | 92 99 94 93 94 92 95 96 342 | 94 92 96 95 97 90 99 98 343 | 344 | 0 !NDON: donors 345 | 346 | 347 | 0 !NACC: acceptors 348 | 349 | 350 | 0 !NNB 351 | 352 | 0 0 0 0 0 0 0 0 353 | 0 0 0 0 0 0 0 0 354 | 0 0 0 0 0 0 0 0 355 | 0 0 0 0 0 0 0 0 356 | 0 0 0 0 0 0 0 0 357 | 0 0 0 0 0 0 0 0 358 | 0 0 0 0 0 0 0 0 359 | 0 0 0 0 0 0 0 0 360 | 0 0 0 0 0 0 0 0 361 | 0 0 0 0 0 0 0 0 362 | 0 0 0 0 0 0 0 0 363 | 0 0 0 0 0 0 0 0 364 | 0 0 0 0 0 0 0 0 365 | 366 | 367 | 1 0 !NGRP 368 | 0 0 0 369 | 370 | -------------------------------------------------------------------------------- /NAMD_Colvars/meta-eABF/Distance.in: -------------------------------------------------------------------------------- 1 | colvarsTrajFrequency 1000 2 | colvarsRestartFrequency 50000 3 | 4 | colvar { 5 | name AtomDistance 6 | 7 | width 0.1 8 | 9 | lowerboundary 12.0 10 | upperboundary 32.0 11 | 12 | lowerwallconstant 10.0 13 | upperwallconstant 10.0 14 | 15 | extendedLagrangian on 16 | extendedFluctuation 0.1 17 | 18 | subtractAppliedForce on 19 | expandBoundaries on 20 | 21 | distance { 22 | group1 { 23 | atomnumbers { 10 } 24 | } 25 | group2 { 26 | atomnumbers { 92 } 27 | } 28 | } 29 | } 30 | 31 | 32 | abf { 33 | colvars AtomDistance 34 | fullSamples 500 35 | } 36 | 37 | metadynamics { 38 | colvars AtomDistance 39 | hillWeight 0.1 40 | hillWidth 3 41 | } -------------------------------------------------------------------------------- /NAMD_Colvars/meta-eABF/abf.conf: -------------------------------------------------------------------------------- 1 | ################################################## 2 | ################################################## 3 | # 4 | # ABF calculation 5 | # 6 | # Deca-alanine 7 | # 8 | ################################################## 9 | ################################################## 10 | 11 | 12 | ################################################## 13 | # MD SECTION 14 | ################################################## 15 | 16 | 17 | # NUMBER OF MD-STEPS 18 | 19 | numsteps 20000000 20 | 21 | 22 | # TOPOLOGY 23 | 24 | structure deca-ala.psf 25 | 26 | 27 | # FORCE FIELD 28 | 29 | parameters par_all22_prot.inp 30 | paraTypeCharmm on 31 | 32 | 33 | # 1-4 TERMs 34 | 35 | exclude scaled1-4 36 | 1-4scaling 1.0 37 | 38 | 39 | # INPUT FILES 40 | 41 | coordinates deca-ala.pdb 42 | 43 | temperature 300.0 44 | 45 | # OUTPUT FILES 46 | 47 | outputname output/abf 48 | 49 | 50 | # FREQUENCY FOR DUMPING OUTPUT DATA 51 | 52 | outputenergies 1000 53 | outputtiming 1000 54 | outputpressure 1000 55 | restartfreq 1000 56 | XSTFreq 1000 57 | dcdFreq 1000 58 | 59 | 60 | # CUT-OFFs 61 | 62 | hgroupcutoff 2.8 63 | switching on 64 | switchdist 10.0 65 | cutoff 12.0 66 | pairlistdist 14.0 67 | 68 | 69 | # CONSTANT-T 70 | 71 | langevin on 72 | langevintemp 300.0 73 | langevindamping 1.0 74 | 75 | 76 | # MULTIPLE TIME-STEP PROPAGATOR 77 | 78 | timestep 0.5 79 | 80 | 81 | # SHAKE/RATTLE 82 | 83 | rigidbonds none 84 | 85 | 86 | # PARALLELISM 87 | 88 | stepspercycle 16 89 | splitpatch hydrogen 90 | margin 2.0 91 | 92 | 93 | # ABF SECTION 94 | 95 | colvars on 96 | colvarsConfig Distance.in 97 | -------------------------------------------------------------------------------- /NAMD_Colvars/meta-eABF/deca-ala.pdb: -------------------------------------------------------------------------------- 1 | REMARK FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 50000 2 | ATOM 1 N ALA B 1 0.113 -2.288 -1.254 1.00 0.00 BH 3 | ATOM 2 HT2 ALA B 1 -0.779 -1.974 -1.687 1.00 0.00 BH 4 | ATOM 3 HT3 ALA B 1 0.803 -2.829 -1.813 1.00 0.00 BH 5 | ATOM 4 CA ALA B 1 0.767 -1.116 -0.506 1.00 0.00 BH 6 | ATOM 5 HA ALA B 1 1.714 -1.559 -0.234 1.00 0.00 BH 7 | ATOM 6 CB ALA B 1 0.790 0.006 -1.515 1.00 0.00 BH 8 | ATOM 7 HB1 ALA B 1 1.247 0.922 -1.085 1.00 0.00 BH 9 | ATOM 8 HB2 ALA B 1 1.323 -0.411 -2.396 1.00 0.00 BH 10 | ATOM 9 HB3 ALA B 1 -0.176 0.421 -1.873 1.00 0.00 BH 11 | ATOM 10 C ALA B 1 -0.064 -0.634 0.728 1.00 0.00 BH 12 | ATOM 11 O ALA B 1 -1.283 -0.502 0.585 1.00 0.00 BH 13 | ATOM 12 N ALA B 2 0.567 -0.384 1.892 1.00 0.00 BH 14 | ATOM 13 HN ALA B 2 1.558 -0.447 1.979 1.00 0.00 BH 15 | ATOM 14 CA ALA B 2 -0.136 -0.308 3.124 1.00 0.00 BH 16 | ATOM 15 HA ALA B 2 -0.582 -1.269 3.333 1.00 0.00 BH 17 | ATOM 16 CB ALA B 2 0.894 -0.058 4.221 1.00 0.00 BH 18 | ATOM 17 HB1 ALA B 2 0.586 0.170 5.264 1.00 0.00 BH 19 | ATOM 18 HB2 ALA B 2 1.386 -1.043 4.368 1.00 0.00 BH 20 | ATOM 19 HB3 ALA B 2 1.572 0.761 3.896 1.00 0.00 BH 21 | ATOM 20 C ALA B 2 -1.193 0.854 3.162 1.00 0.00 BH 22 | ATOM 21 O ALA B 2 -2.372 0.602 3.566 1.00 0.00 BH 23 | ATOM 22 N ALA B 3 -0.856 2.141 2.875 1.00 0.00 BH 24 | ATOM 23 HN ALA B 3 0.082 2.422 2.689 1.00 0.00 BH 25 | ATOM 24 CA ALA B 3 -1.733 3.280 2.950 1.00 0.00 BH 26 | ATOM 25 HA ALA B 3 -1.997 3.414 3.989 1.00 0.00 BH 27 | ATOM 26 CB ALA B 3 -0.919 4.499 2.477 1.00 0.00 BH 28 | ATOM 27 HB1 ALA B 3 -0.655 4.413 1.401 1.00 0.00 BH 29 | ATOM 28 HB2 ALA B 3 -1.373 5.496 2.661 1.00 0.00 BH 30 | ATOM 29 HB3 ALA B 3 0.046 4.517 3.027 1.00 0.00 BH 31 | ATOM 30 C ALA B 3 -3.066 3.199 2.243 1.00 0.00 BH 32 | ATOM 31 O ALA B 3 -4.119 3.466 2.841 1.00 0.00 BH 33 | ATOM 32 N ALA B 4 -3.071 2.558 1.079 1.00 0.00 BH 34 | ATOM 33 HN ALA B 4 -2.166 2.271 0.776 1.00 0.00 BH 35 | ATOM 34 CA ALA B 4 -4.295 2.275 0.353 1.00 0.00 BH 36 | ATOM 35 HA ALA B 4 -4.896 3.161 0.210 1.00 0.00 BH 37 | ATOM 36 CB ALA B 4 -3.971 1.919 -1.163 1.00 0.00 BH 38 | ATOM 37 HB1 ALA B 4 -3.481 2.802 -1.626 1.00 0.00 BH 39 | ATOM 38 HB2 ALA B 4 -3.239 1.084 -1.214 1.00 0.00 BH 40 | ATOM 39 HB3 ALA B 4 -4.905 1.551 -1.638 1.00 0.00 BH 41 | ATOM 40 C ALA B 4 -5.138 1.148 1.014 1.00 0.00 BH 42 | ATOM 41 O ALA B 4 -6.290 1.290 1.505 1.00 0.00 BH 43 | ATOM 42 N ALA B 5 -4.485 -0.069 0.981 1.00 0.00 BH 44 | ATOM 43 HN ALA B 5 -3.535 -0.144 0.687 1.00 0.00 BH 45 | ATOM 44 CA ALA B 5 -4.953 -1.327 1.563 1.00 0.00 BH 46 | ATOM 45 HA ALA B 5 -5.600 -1.791 0.833 1.00 0.00 BH 47 | ATOM 46 CB ALA B 5 -3.792 -2.416 1.640 1.00 0.00 BH 48 | ATOM 47 HB1 ALA B 5 -3.238 -2.513 0.682 1.00 0.00 BH 49 | ATOM 48 HB2 ALA B 5 -3.051 -2.249 2.451 1.00 0.00 BH 50 | ATOM 49 HB3 ALA B 5 -4.151 -3.455 1.805 1.00 0.00 BH 51 | ATOM 50 C ALA B 5 -5.728 -1.269 2.853 1.00 0.00 BH 52 | ATOM 51 O ALA B 5 -6.821 -1.826 3.026 1.00 0.00 BH 53 | ATOM 52 N ALA B 6 -5.092 -0.721 3.920 1.00 0.00 BH 54 | ATOM 53 HN ALA B 6 -4.250 -0.199 3.808 1.00 0.00 BH 55 | ATOM 54 CA ALA B 6 -5.756 -0.450 5.212 1.00 0.00 BH 56 | ATOM 55 HA ALA B 6 -6.319 -1.344 5.435 1.00 0.00 BH 57 | ATOM 56 CB ALA B 6 -4.701 -0.089 6.243 1.00 0.00 BH 58 | ATOM 57 HB1 ALA B 6 -4.174 0.836 5.923 1.00 0.00 BH 59 | ATOM 58 HB2 ALA B 6 -5.122 -0.006 7.268 1.00 0.00 BH 60 | ATOM 59 HB3 ALA B 6 -4.066 -0.993 6.365 1.00 0.00 BH 61 | ATOM 60 C ALA B 6 -6.839 0.547 5.134 1.00 0.00 BH 62 | ATOM 61 O ALA B 6 -7.796 0.344 5.789 1.00 0.00 BH 63 | ATOM 62 N ALA B 7 -6.709 1.632 4.377 1.00 0.00 BH 64 | ATOM 63 HN ALA B 7 -5.900 1.830 3.830 1.00 0.00 BH 65 | ATOM 64 CA ALA B 7 -7.707 2.606 4.337 1.00 0.00 BH 66 | ATOM 65 HA ALA B 7 -8.028 2.824 5.345 1.00 0.00 BH 67 | ATOM 66 CB ALA B 7 -6.920 3.781 3.934 1.00 0.00 BH 68 | ATOM 67 HB1 ALA B 7 -6.703 3.722 2.846 1.00 0.00 BH 69 | ATOM 68 HB2 ALA B 7 -7.445 4.746 4.096 1.00 0.00 BH 70 | ATOM 69 HB3 ALA B 7 -5.940 3.795 4.458 1.00 0.00 BH 71 | ATOM 70 C ALA B 7 -8.912 2.354 3.463 1.00 0.00 BH 72 | ATOM 71 O ALA B 7 -9.974 2.853 3.663 1.00 0.00 BH 73 | ATOM 72 N ALA B 8 -8.864 1.404 2.514 1.00 0.00 BH 74 | ATOM 73 HN ALA B 8 -7.932 1.244 2.200 1.00 0.00 BH 75 | ATOM 74 CA ALA B 8 -10.008 0.910 1.816 1.00 0.00 BH 76 | ATOM 75 HA ALA B 8 -10.785 1.635 1.621 1.00 0.00 BH 77 | ATOM 76 CB ALA B 8 -9.572 0.291 0.457 1.00 0.00 BH 78 | ATOM 77 HB1 ALA B 8 -10.397 -0.326 0.040 1.00 0.00 BH 79 | ATOM 78 HB2 ALA B 8 -9.311 1.110 -0.247 1.00 0.00 BH 80 | ATOM 79 HB3 ALA B 8 -8.793 -0.479 0.643 1.00 0.00 BH 81 | ATOM 80 C ALA B 8 -10.663 -0.166 2.707 1.00 0.00 BH 82 | ATOM 81 O ALA B 8 -11.882 -0.432 2.666 1.00 0.00 BH 83 | ATOM 82 N ALA B 9 -9.886 -0.789 3.580 1.00 0.00 BH 84 | ATOM 83 HN ALA B 9 -8.904 -0.621 3.609 1.00 0.00 BH 85 | ATOM 84 CA ALA B 9 -10.404 -1.774 4.539 1.00 0.00 BH 86 | ATOM 85 HA ALA B 9 -10.996 -2.532 4.049 1.00 0.00 BH 87 | ATOM 86 CB ALA B 9 -9.238 -2.543 5.191 1.00 0.00 BH 88 | ATOM 87 HB1 ALA B 9 -8.806 -3.097 4.331 1.00 0.00 BH 89 | ATOM 88 HB2 ALA B 9 -8.467 -1.819 5.532 1.00 0.00 BH 90 | ATOM 89 HB3 ALA B 9 -9.463 -3.262 6.007 1.00 0.00 BH 91 | ATOM 90 C ALA B 9 -11.212 -1.063 5.618 1.00 0.00 BH 92 | ATOM 91 O ALA B 9 -12.370 -1.417 5.769 1.00 0.00 BH 93 | ATOM 92 C ALA B 10 -11.957 1.980 7.072 1.00 0.00 BH 94 | ATOM 93 O ALA B 10 -11.964 3.008 7.760 1.00 0.00 BH 95 | ATOM 94 NT ALA B 10 -12.813 1.968 5.971 1.00 0.00 BH 96 | ATOM 95 HT1 ALA B 10 -13.399 2.748 5.755 1.00 0.00 BH 97 | ATOM 96 HT2 ALA B 10 -12.618 1.237 5.316 1.00 0.00 BH 98 | ATOM 97 N ALA B 10 -10.690 0.020 6.213 1.00 0.00 BH 99 | ATOM 98 HN ALA B 10 -9.720 0.133 6.012 1.00 0.00 BH 100 | ATOM 99 CA ALA B 10 -11.166 0.664 7.402 1.00 0.00 BH 101 | ATOM 100 HA ALA B 10 -11.936 0.058 7.856 1.00 0.00 BH 102 | ATOM 101 CB ALA B 10 -10.058 0.920 8.404 1.00 0.00 BH 103 | ATOM 102 HB1 ALA B 10 -9.202 1.387 7.871 1.00 0.00 BH 104 | ATOM 103 HB2 ALA B 10 -10.427 1.550 9.242 1.00 0.00 BH 105 | ATOM 104 HB3 ALA B 10 -9.603 -0.048 8.702 1.00 0.00 BH 106 | END 107 | -------------------------------------------------------------------------------- /NAMD_Colvars/meta-eABF/deca-ala.psf: -------------------------------------------------------------------------------- 1 | PSF 2 | 3 | 1 !NTITLE 4 | REMARKS original generated structure x-plor psf file 5 | 6 | 104 !NATOM 7 | 1 BH 1 ALA N NH3 -0.620000 14.0070 0 8 | 2 BH 1 ALA HT2 HC 0.310000 1.0080 0 9 | 3 BH 1 ALA HT3 HC 0.310000 1.0080 0 10 | 4 BH 1 ALA CA CT1 -0.100000 12.0110 0 11 | 5 BH 1 ALA HA HB 0.100000 1.0080 0 12 | 6 BH 1 ALA CB CT3 -0.270000 12.0110 0 13 | 7 BH 1 ALA HB1 HA 0.090000 1.0080 0 14 | 8 BH 1 ALA HB2 HA 0.090000 1.0080 0 15 | 9 BH 1 ALA HB3 HA 0.090000 1.0080 0 16 | 10 BH 1 ALA C C 0.510000 12.0110 0 17 | 11 BH 1 ALA O O -0.510000 15.9990 0 18 | 12 BH 2 ALA N NH1 -0.470000 14.0070 0 19 | 13 BH 2 ALA HN H 0.310000 1.0080 0 20 | 14 BH 2 ALA CA CT1 0.070000 12.0110 0 21 | 15 BH 2 ALA HA HB 0.090000 1.0080 0 22 | 16 BH 2 ALA CB CT3 -0.270000 12.0110 0 23 | 17 BH 2 ALA HB1 HA 0.090000 1.0080 0 24 | 18 BH 2 ALA HB2 HA 0.090000 1.0080 0 25 | 19 BH 2 ALA HB3 HA 0.090000 1.0080 0 26 | 20 BH 2 ALA C C 0.510000 12.0110 0 27 | 21 BH 2 ALA O O -0.510000 15.9990 0 28 | 22 BH 3 ALA N NH1 -0.470000 14.0070 0 29 | 23 BH 3 ALA HN H 0.310000 1.0080 0 30 | 24 BH 3 ALA CA CT1 0.070000 12.0110 0 31 | 25 BH 3 ALA HA HB 0.090000 1.0080 0 32 | 26 BH 3 ALA CB CT3 -0.270000 12.0110 0 33 | 27 BH 3 ALA HB1 HA 0.090000 1.0080 0 34 | 28 BH 3 ALA HB2 HA 0.090000 1.0080 0 35 | 29 BH 3 ALA HB3 HA 0.090000 1.0080 0 36 | 30 BH 3 ALA C C 0.510000 12.0110 0 37 | 31 BH 3 ALA O O -0.510000 15.9990 0 38 | 32 BH 4 ALA N NH1 -0.470000 14.0070 0 39 | 33 BH 4 ALA HN H 0.310000 1.0080 0 40 | 34 BH 4 ALA CA CT1 0.070000 12.0110 0 41 | 35 BH 4 ALA HA HB 0.090000 1.0080 0 42 | 36 BH 4 ALA CB CT3 -0.270000 12.0110 0 43 | 37 BH 4 ALA HB1 HA 0.090000 1.0080 0 44 | 38 BH 4 ALA HB2 HA 0.090000 1.0080 0 45 | 39 BH 4 ALA HB3 HA 0.090000 1.0080 0 46 | 40 BH 4 ALA C C 0.510000 12.0110 0 47 | 41 BH 4 ALA O O -0.510000 15.9990 0 48 | 42 BH 5 ALA N NH1 -0.470000 14.0070 0 49 | 43 BH 5 ALA HN H 0.310000 1.0080 0 50 | 44 BH 5 ALA CA CT1 0.070000 12.0110 0 51 | 45 BH 5 ALA HA HB 0.090000 1.0080 0 52 | 46 BH 5 ALA CB CT3 -0.270000 12.0110 0 53 | 47 BH 5 ALA HB1 HA 0.090000 1.0080 0 54 | 48 BH 5 ALA HB2 HA 0.090000 1.0080 0 55 | 49 BH 5 ALA HB3 HA 0.090000 1.0080 0 56 | 50 BH 5 ALA C C 0.510000 12.0110 0 57 | 51 BH 5 ALA O O -0.510000 15.9990 0 58 | 52 BH 6 ALA N NH1 -0.470000 14.0070 0 59 | 53 BH 6 ALA HN H 0.310000 1.0080 0 60 | 54 BH 6 ALA CA CT1 0.070000 12.0110 0 61 | 55 BH 6 ALA HA HB 0.090000 1.0080 0 62 | 56 BH 6 ALA CB CT3 -0.270000 12.0110 0 63 | 57 BH 6 ALA HB1 HA 0.090000 1.0080 0 64 | 58 BH 6 ALA HB2 HA 0.090000 1.0080 0 65 | 59 BH 6 ALA HB3 HA 0.090000 1.0080 0 66 | 60 BH 6 ALA C C 0.510000 12.0110 0 67 | 61 BH 6 ALA O O -0.510000 15.9990 0 68 | 62 BH 7 ALA N NH1 -0.470000 14.0070 0 69 | 63 BH 7 ALA HN H 0.310000 1.0080 0 70 | 64 BH 7 ALA CA CT1 0.070000 12.0110 0 71 | 65 BH 7 ALA HA HB 0.090000 1.0080 0 72 | 66 BH 7 ALA CB CT3 -0.270000 12.0110 0 73 | 67 BH 7 ALA HB1 HA 0.090000 1.0080 0 74 | 68 BH 7 ALA HB2 HA 0.090000 1.0080 0 75 | 69 BH 7 ALA HB3 HA 0.090000 1.0080 0 76 | 70 BH 7 ALA C C 0.510000 12.0110 0 77 | 71 BH 7 ALA O O -0.510000 15.9990 0 78 | 72 BH 8 ALA N NH1 -0.470000 14.0070 0 79 | 73 BH 8 ALA HN H 0.310000 1.0080 0 80 | 74 BH 8 ALA CA CT1 0.070000 12.0110 0 81 | 75 BH 8 ALA HA HB 0.090000 1.0080 0 82 | 76 BH 8 ALA CB CT3 -0.270000 12.0110 0 83 | 77 BH 8 ALA HB1 HA 0.090000 1.0080 0 84 | 78 BH 8 ALA HB2 HA 0.090000 1.0080 0 85 | 79 BH 8 ALA HB3 HA 0.090000 1.0080 0 86 | 80 BH 8 ALA C C 0.510000 12.0110 0 87 | 81 BH 8 ALA O O -0.510000 15.9990 0 88 | 82 BH 9 ALA N NH1 -0.470000 14.0070 0 89 | 83 BH 9 ALA HN H 0.310000 1.0080 0 90 | 84 BH 9 ALA CA CT1 0.070000 12.0110 0 91 | 85 BH 9 ALA HA HB 0.090000 1.0080 0 92 | 86 BH 9 ALA CB CT3 -0.270000 12.0110 0 93 | 87 BH 9 ALA HB1 HA 0.090000 1.0080 0 94 | 88 BH 9 ALA HB2 HA 0.090000 1.0080 0 95 | 89 BH 9 ALA HB3 HA 0.090000 1.0080 0 96 | 90 BH 9 ALA C C 0.510000 12.0110 0 97 | 91 BH 9 ALA O O -0.510000 15.9990 0 98 | 92 BH 10 ALA C CC 0.550000 12.0110 0 99 | 93 BH 10 ALA O O -0.550000 15.9990 0 100 | 94 BH 10 ALA NT NH2 -0.620000 14.0070 0 101 | 95 BH 10 ALA HT1 H 0.320000 1.0080 0 102 | 96 BH 10 ALA HT2 H 0.300000 1.0080 0 103 | 97 BH 10 ALA N NH1 -0.470000 14.0070 0 104 | 98 BH 10 ALA HN H 0.310000 1.0080 0 105 | 99 BH 10 ALA CA CT1 0.070000 12.0110 0 106 | 100 BH 10 ALA HA HB 0.090000 1.0080 0 107 | 101 BH 10 ALA CB CT3 -0.270000 12.0110 0 108 | 102 BH 10 ALA HB1 HA 0.090000 1.0080 0 109 | 103 BH 10 ALA HB2 HA 0.090000 1.0080 0 110 | 104 BH 10 ALA HB3 HA 0.090000 1.0080 0 111 | 112 | 103 !NBOND: bonds 113 | 1 4 2 1 3 1 4 5 114 | 6 4 6 7 6 8 6 9 115 | 10 4 10 12 11 10 12 13 116 | 12 14 14 15 16 14 16 17 117 | 16 18 16 19 20 14 20 22 118 | 21 20 22 23 22 24 24 25 119 | 26 24 26 27 26 28 26 29 120 | 30 24 30 32 31 30 32 33 121 | 32 34 34 35 36 34 36 37 122 | 36 38 36 39 40 34 40 42 123 | 41 40 42 43 42 44 44 45 124 | 46 44 46 47 46 48 46 49 125 | 50 44 50 52 51 50 52 53 126 | 52 54 54 55 56 54 56 57 127 | 56 58 56 59 60 54 60 62 128 | 61 60 62 63 62 64 64 65 129 | 66 64 66 67 66 68 66 69 130 | 70 64 70 72 71 70 72 73 131 | 72 74 74 75 76 74 76 77 132 | 76 78 76 79 80 74 80 82 133 | 81 80 82 83 82 84 84 85 134 | 86 84 86 87 86 88 86 89 135 | 90 84 90 97 91 90 92 94 136 | 92 99 93 92 94 95 94 96 137 | 97 98 97 99 99 100 101 99 138 | 101 102 101 103 101 104 139 | 140 | 183 !NTHETA: angles 141 | 1 4 5 1 4 10 2 1 4 142 | 2 1 3 3 1 4 4 10 11 143 | 4 10 12 4 6 9 4 6 8 144 | 4 6 7 6 4 5 6 4 10 145 | 6 4 1 7 6 9 7 6 8 146 | 8 6 9 10 4 5 12 14 15 147 | 12 14 20 12 10 11 13 12 10 148 | 13 12 14 14 20 21 14 20 22 149 | 14 16 19 14 16 18 14 16 17 150 | 14 12 10 16 14 15 16 14 20 151 | 16 14 12 17 16 19 17 16 18 152 | 18 16 19 20 14 15 22 24 25 153 | 22 24 30 22 20 21 23 22 20 154 | 23 22 24 24 30 31 24 30 32 155 | 24 26 29 24 26 28 24 26 27 156 | 24 22 20 26 24 25 26 24 30 157 | 26 24 22 27 26 29 27 26 28 158 | 28 26 29 30 24 25 32 34 35 159 | 32 34 40 32 30 31 33 32 30 160 | 33 32 34 34 40 41 34 40 42 161 | 34 36 39 34 36 38 34 36 37 162 | 34 32 30 36 34 35 36 34 40 163 | 36 34 32 37 36 39 37 36 38 164 | 38 36 39 40 34 35 42 44 45 165 | 42 44 50 42 40 41 43 42 40 166 | 43 42 44 44 50 51 44 50 52 167 | 44 46 49 44 46 48 44 46 47 168 | 44 42 40 46 44 45 46 44 50 169 | 46 44 42 47 46 49 47 46 48 170 | 48 46 49 50 44 45 52 54 55 171 | 52 54 60 52 50 51 53 52 50 172 | 53 52 54 54 60 61 54 60 62 173 | 54 56 59 54 56 58 54 56 57 174 | 54 52 50 56 54 55 56 54 60 175 | 56 54 52 57 56 59 57 56 58 176 | 58 56 59 60 54 55 62 64 65 177 | 62 64 70 62 60 61 63 62 60 178 | 63 62 64 64 70 71 64 70 72 179 | 64 66 69 64 66 68 64 66 67 180 | 64 62 60 66 64 65 66 64 70 181 | 66 64 62 67 66 69 67 66 68 182 | 68 66 69 70 64 65 72 74 75 183 | 72 74 80 72 70 71 73 72 70 184 | 73 72 74 74 80 81 74 80 82 185 | 74 76 79 74 76 78 74 76 77 186 | 74 72 70 76 74 75 76 74 80 187 | 76 74 72 77 76 79 77 76 78 188 | 78 76 79 80 74 75 82 84 85 189 | 82 84 90 82 80 81 83 82 80 190 | 83 82 84 84 90 91 84 90 97 191 | 84 86 89 84 86 88 84 86 87 192 | 84 82 80 86 84 85 86 84 90 193 | 86 84 82 87 86 89 87 86 88 194 | 88 86 89 90 84 85 92 99 100 195 | 92 94 96 92 94 95 94 92 93 196 | 94 92 99 95 94 96 97 99 100 197 | 97 99 92 97 90 91 98 97 90 198 | 98 97 99 99 101 104 99 101 103 199 | 99 101 102 99 97 90 99 92 93 200 | 101 99 100 101 99 92 101 99 97 201 | 102 101 104 102 101 103 103 101 104 202 | 203 | 251 !NPHI: dihedrals 204 | 1 4 6 7 1 4 6 8 205 | 1 4 6 9 1 4 10 12 206 | 1 4 10 11 2 1 4 6 207 | 2 1 4 10 2 1 4 5 208 | 3 1 4 6 3 1 4 10 209 | 3 1 4 5 4 10 12 13 210 | 4 10 12 14 5 4 6 7 211 | 5 4 6 8 5 4 6 9 212 | 5 4 10 12 5 4 10 11 213 | 6 4 10 12 6 4 10 11 214 | 7 6 4 10 8 6 4 10 215 | 9 6 4 10 10 12 14 16 216 | 10 12 14 20 10 12 14 15 217 | 11 10 12 13 11 10 12 14 218 | 12 14 16 17 12 14 16 18 219 | 12 14 16 19 12 14 20 22 220 | 12 14 20 21 13 12 14 16 221 | 13 12 14 20 13 12 14 15 222 | 14 20 22 23 14 20 22 24 223 | 15 14 16 17 15 14 16 18 224 | 15 14 16 19 15 14 20 22 225 | 15 14 20 21 16 14 20 22 226 | 16 14 20 21 17 16 14 20 227 | 18 16 14 20 19 16 14 20 228 | 20 22 24 26 20 22 24 30 229 | 20 22 24 25 21 20 22 23 230 | 21 20 22 24 22 24 26 27 231 | 22 24 26 28 22 24 26 29 232 | 22 24 30 32 22 24 30 31 233 | 23 22 24 26 23 22 24 30 234 | 23 22 24 25 24 30 32 33 235 | 24 30 32 34 25 24 26 27 236 | 25 24 26 28 25 24 26 29 237 | 25 24 30 32 25 24 30 31 238 | 26 24 30 32 26 24 30 31 239 | 27 26 24 30 28 26 24 30 240 | 29 26 24 30 30 32 34 36 241 | 30 32 34 40 30 32 34 35 242 | 31 30 32 33 31 30 32 34 243 | 32 34 36 37 32 34 36 38 244 | 32 34 36 39 32 34 40 42 245 | 32 34 40 41 33 32 34 36 246 | 33 32 34 40 33 32 34 35 247 | 34 40 42 43 34 40 42 44 248 | 35 34 36 37 35 34 36 38 249 | 35 34 36 39 35 34 40 42 250 | 35 34 40 41 36 34 40 42 251 | 36 34 40 41 37 36 34 40 252 | 38 36 34 40 39 36 34 40 253 | 40 42 44 46 40 42 44 50 254 | 40 42 44 45 41 40 42 43 255 | 41 40 42 44 42 44 46 47 256 | 42 44 46 48 42 44 46 49 257 | 42 44 50 52 42 44 50 51 258 | 43 42 44 46 43 42 44 50 259 | 43 42 44 45 44 50 52 53 260 | 44 50 52 54 45 44 46 47 261 | 45 44 46 48 45 44 46 49 262 | 45 44 50 52 45 44 50 51 263 | 46 44 50 52 46 44 50 51 264 | 47 46 44 50 48 46 44 50 265 | 49 46 44 50 50 52 54 56 266 | 50 52 54 60 50 52 54 55 267 | 51 50 52 53 51 50 52 54 268 | 52 54 56 57 52 54 56 58 269 | 52 54 56 59 52 54 60 62 270 | 52 54 60 61 53 52 54 56 271 | 53 52 54 60 53 52 54 55 272 | 54 60 62 63 54 60 62 64 273 | 55 54 56 57 55 54 56 58 274 | 55 54 56 59 55 54 60 62 275 | 55 54 60 61 56 54 60 62 276 | 56 54 60 61 57 56 54 60 277 | 58 56 54 60 59 56 54 60 278 | 60 62 64 66 60 62 64 70 279 | 60 62 64 65 61 60 62 63 280 | 61 60 62 64 62 64 66 67 281 | 62 64 66 68 62 64 66 69 282 | 62 64 70 72 62 64 70 71 283 | 63 62 64 66 63 62 64 70 284 | 63 62 64 65 64 70 72 73 285 | 64 70 72 74 65 64 66 67 286 | 65 64 66 68 65 64 66 69 287 | 65 64 70 72 65 64 70 71 288 | 66 64 70 72 66 64 70 71 289 | 67 66 64 70 68 66 64 70 290 | 69 66 64 70 70 72 74 76 291 | 70 72 74 80 70 72 74 75 292 | 71 70 72 73 71 70 72 74 293 | 72 74 76 77 72 74 76 78 294 | 72 74 76 79 72 74 80 82 295 | 72 74 80 81 73 72 74 76 296 | 73 72 74 80 73 72 74 75 297 | 74 80 82 83 74 80 82 84 298 | 75 74 76 77 75 74 76 78 299 | 75 74 76 79 75 74 80 82 300 | 75 74 80 81 76 74 80 82 301 | 76 74 80 81 77 76 74 80 302 | 78 76 74 80 79 76 74 80 303 | 80 82 84 86 80 82 84 90 304 | 80 82 84 85 81 80 82 83 305 | 81 80 82 84 82 84 86 87 306 | 82 84 86 88 82 84 86 89 307 | 82 84 90 97 82 84 90 91 308 | 83 82 84 86 83 82 84 90 309 | 83 82 84 85 84 90 97 98 310 | 84 90 97 99 85 84 86 87 311 | 85 84 86 88 85 84 86 89 312 | 85 84 90 97 85 84 90 91 313 | 86 84 90 97 86 84 90 91 314 | 87 86 84 90 88 86 84 90 315 | 89 86 84 90 90 97 99 101 316 | 90 97 99 92 90 97 99 100 317 | 91 90 97 98 91 90 97 99 318 | 92 99 101 102 92 99 101 103 319 | 92 99 101 104 92 99 97 98 320 | 93 92 94 95 93 92 94 96 321 | 93 92 99 101 93 92 99 97 322 | 93 92 99 100 94 92 99 101 323 | 94 92 99 97 94 92 99 100 324 | 95 94 92 99 96 94 92 99 325 | 97 99 101 102 97 99 101 103 326 | 97 99 101 104 98 97 99 101 327 | 98 97 99 100 99 92 94 96 328 | 100 99 101 102 100 99 101 103 329 | 100 99 101 104 330 | 331 | 22 !NIMPHI: impropers 332 | 10 4 12 11 12 10 14 13 333 | 20 14 22 21 22 20 24 23 334 | 30 24 32 31 32 30 34 33 335 | 40 34 42 41 42 40 44 43 336 | 50 44 52 51 52 50 54 53 337 | 60 54 62 61 62 60 64 63 338 | 70 64 72 71 72 70 74 73 339 | 80 74 82 81 82 80 84 83 340 | 90 84 97 91 92 94 99 93 341 | 92 99 94 93 94 92 95 96 342 | 94 92 96 95 97 90 99 98 343 | 344 | 0 !NDON: donors 345 | 346 | 347 | 0 !NACC: acceptors 348 | 349 | 350 | 0 !NNB 351 | 352 | 0 0 0 0 0 0 0 0 353 | 0 0 0 0 0 0 0 0 354 | 0 0 0 0 0 0 0 0 355 | 0 0 0 0 0 0 0 0 356 | 0 0 0 0 0 0 0 0 357 | 0 0 0 0 0 0 0 0 358 | 0 0 0 0 0 0 0 0 359 | 0 0 0 0 0 0 0 0 360 | 0 0 0 0 0 0 0 0 361 | 0 0 0 0 0 0 0 0 362 | 0 0 0 0 0 0 0 0 363 | 0 0 0 0 0 0 0 0 364 | 0 0 0 0 0 0 0 0 365 | 366 | 367 | 1 0 !NGRP 368 | 0 0 0 369 | 370 | -------------------------------------------------------------------------------- /Openmm_Plumed/WTM-eABF/OpenMM_conf.py: -------------------------------------------------------------------------------- 1 | from simtk.openmm.app import * 2 | from simtk.openmm import * 3 | from simtk.unit import * 4 | from sys import stdout, exit, stderr 5 | 6 | platform = Platform.getPlatformByName('CPU') 7 | 8 | psf = CharmmPsfFile('deca-ala.psf') 9 | pdb = PDBFile('deca-ala.pdb') 10 | params = CharmmParameterSet(par_all22_prot.inp) 11 | system = psf.createSystem( 12 | params, 13 | nonbondedCutoff=1.2*nanometer, 14 | switchDistance=1.0*nanometer, 15 | hydrogenMass=1.008*amu) 16 | from openmmplumed import * 17 | import colvars 18 | system.addForce(PlumedForce(colvars.script)) 19 | integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.0005*picoseconds) 20 | simulation = Simulation(psf.topology, system, integrator, platform, properties) 21 | simulation.context.setPositions(pdb.positions) 22 | simulation.minimizeEnergy() 23 | simulation.reporters.append(DCDReporter('output/abf.dcd', 1000)) 24 | simulation.reporters.append(CheckpointReporter('output/abf.chk', 1000)) 25 | simulation.reporters.append(StateDataReporter( 26 | stdout, 27 | 1000, 28 | step=True, 29 | volume=True, 30 | density=True, 31 | potentialEnergy=True, 32 | temperature=True, 33 | speed=True, 34 | remainingTime=True, 35 | totalSteps=20000000)) 36 | simulation.step(20000000) 37 | -------------------------------------------------------------------------------- /Openmm_Plumed/WTM-eABF/abf.py: -------------------------------------------------------------------------------- 1 | from simtk.openmm.app import * 2 | from simtk.openmm import * 3 | from simtk.unit import * 4 | from sys import stdout, exit, stderr 5 | 6 | platform = Platform.getPlatformByName('CPU') 7 | properties = {'Threads': '2'} 8 | 9 | psf = CharmmPsfFile('deca-ala.psf') 10 | pdb = PDBFile('deca-ala.pdb') 11 | params = CharmmParameterSet('top_all22_prot.inp','par_all22_prot.inp') 12 | system = psf.createSystem( 13 | params, 14 | nonbondedCutoff=1.2*nanometer, 15 | switchDistance=1.0*nanometer, 16 | hydrogenMass=1.008*amu) 17 | from openmmplumed import * 18 | import colvars 19 | system.addForce(PlumedForce(colvars.script)) 20 | integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.0005*picoseconds) 21 | simulation = Simulation(psf.topology, system, integrator, platform, properties) 22 | simulation.context.setPositions(pdb.positions) 23 | simulation.minimizeEnergy() 24 | simulation.reporters.append(DCDReporter('output/abf.dcd', 1000)) 25 | simulation.reporters.append(CheckpointReporter('output/abf.chk', 1000)) 26 | simulation.reporters.append(StateDataReporter( 27 | stdout, 28 | 1000, 29 | step=True, 30 | volume=True, 31 | density=True, 32 | potentialEnergy=True, 33 | temperature=True, 34 | speed=True, 35 | remainingTime=True, 36 | totalSteps=20000000)) 37 | simulation.step(20000000) 38 | -------------------------------------------------------------------------------- /Openmm_Plumed/WTM-eABF/colvars.py: -------------------------------------------------------------------------------- 1 | script = """ 2 | d1: DISTANCE ATOMS=10,92 3 | 4 | eabf: DRR ARG=d1 FULLSAMPLES=500 FRICTION=1.0 TAU=0.2 TEMP=300 TEXTOUTPUT GRID_MIN=1.2 GRID_MAX=3.2 GRID_SPACING=0.01 OUTPUTFREQ=50000 HISTORYFREQ=50000 OUTPUTPREFIX=output/eabf 5 | wtmeabf: METAD ARG=eabf.d1_fict PACE=1000 SIGMA=0.25 HEIGHT=0.4 TEMP=300 BIASFACTOR=14 GRID_MIN=0.7 GRID_MAX=3.7 6 | 7 | uwall: UPPER_WALLS ARG=eabf.d1_fict AT=3.2 KAPPA=300000 8 | lwall: LOWER_WALLS ARG=eabf.d1_fict AT=1.2 KAPPA=300000 9 | 10 | PRINT STRIDE=10000 ARG=d1 FILE=COLVAR 11 | """ 12 | -------------------------------------------------------------------------------- /Openmm_Plumed/WTM-eABF/deca-ala.pdb: -------------------------------------------------------------------------------- 1 | REMARK FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 50000 2 | ATOM 1 N ALA B 1 0.113 -2.288 -1.254 1.00 0.00 BH 3 | ATOM 2 HT2 ALA B 1 -0.779 -1.974 -1.687 1.00 0.00 BH 4 | ATOM 3 HT3 ALA B 1 0.803 -2.829 -1.813 1.00 0.00 BH 5 | ATOM 4 CA ALA B 1 0.767 -1.116 -0.506 1.00 0.00 BH 6 | ATOM 5 HA ALA B 1 1.714 -1.559 -0.234 1.00 0.00 BH 7 | ATOM 6 CB ALA B 1 0.790 0.006 -1.515 1.00 0.00 BH 8 | ATOM 7 HB1 ALA B 1 1.247 0.922 -1.085 1.00 0.00 BH 9 | ATOM 8 HB2 ALA B 1 1.323 -0.411 -2.396 1.00 0.00 BH 10 | ATOM 9 HB3 ALA B 1 -0.176 0.421 -1.873 1.00 0.00 BH 11 | ATOM 10 C ALA B 1 -0.064 -0.634 0.728 1.00 0.00 BH 12 | ATOM 11 O ALA B 1 -1.283 -0.502 0.585 1.00 0.00 BH 13 | ATOM 12 N ALA B 2 0.567 -0.384 1.892 1.00 0.00 BH 14 | ATOM 13 HN ALA B 2 1.558 -0.447 1.979 1.00 0.00 BH 15 | ATOM 14 CA ALA B 2 -0.136 -0.308 3.124 1.00 0.00 BH 16 | ATOM 15 HA ALA B 2 -0.582 -1.269 3.333 1.00 0.00 BH 17 | ATOM 16 CB ALA B 2 0.894 -0.058 4.221 1.00 0.00 BH 18 | ATOM 17 HB1 ALA B 2 0.586 0.170 5.264 1.00 0.00 BH 19 | ATOM 18 HB2 ALA B 2 1.386 -1.043 4.368 1.00 0.00 BH 20 | ATOM 19 HB3 ALA B 2 1.572 0.761 3.896 1.00 0.00 BH 21 | ATOM 20 C ALA B 2 -1.193 0.854 3.162 1.00 0.00 BH 22 | ATOM 21 O ALA B 2 -2.372 0.602 3.566 1.00 0.00 BH 23 | ATOM 22 N ALA B 3 -0.856 2.141 2.875 1.00 0.00 BH 24 | ATOM 23 HN ALA B 3 0.082 2.422 2.689 1.00 0.00 BH 25 | ATOM 24 CA ALA B 3 -1.733 3.280 2.950 1.00 0.00 BH 26 | ATOM 25 HA ALA B 3 -1.997 3.414 3.989 1.00 0.00 BH 27 | ATOM 26 CB ALA B 3 -0.919 4.499 2.477 1.00 0.00 BH 28 | ATOM 27 HB1 ALA B 3 -0.655 4.413 1.401 1.00 0.00 BH 29 | ATOM 28 HB2 ALA B 3 -1.373 5.496 2.661 1.00 0.00 BH 30 | ATOM 29 HB3 ALA B 3 0.046 4.517 3.027 1.00 0.00 BH 31 | ATOM 30 C ALA B 3 -3.066 3.199 2.243 1.00 0.00 BH 32 | ATOM 31 O ALA B 3 -4.119 3.466 2.841 1.00 0.00 BH 33 | ATOM 32 N ALA B 4 -3.071 2.558 1.079 1.00 0.00 BH 34 | ATOM 33 HN ALA B 4 -2.166 2.271 0.776 1.00 0.00 BH 35 | ATOM 34 CA ALA B 4 -4.295 2.275 0.353 1.00 0.00 BH 36 | ATOM 35 HA ALA B 4 -4.896 3.161 0.210 1.00 0.00 BH 37 | ATOM 36 CB ALA B 4 -3.971 1.919 -1.163 1.00 0.00 BH 38 | ATOM 37 HB1 ALA B 4 -3.481 2.802 -1.626 1.00 0.00 BH 39 | ATOM 38 HB2 ALA B 4 -3.239 1.084 -1.214 1.00 0.00 BH 40 | ATOM 39 HB3 ALA B 4 -4.905 1.551 -1.638 1.00 0.00 BH 41 | ATOM 40 C ALA B 4 -5.138 1.148 1.014 1.00 0.00 BH 42 | ATOM 41 O ALA B 4 -6.290 1.290 1.505 1.00 0.00 BH 43 | ATOM 42 N ALA B 5 -4.485 -0.069 0.981 1.00 0.00 BH 44 | ATOM 43 HN ALA B 5 -3.535 -0.144 0.687 1.00 0.00 BH 45 | ATOM 44 CA ALA B 5 -4.953 -1.327 1.563 1.00 0.00 BH 46 | ATOM 45 HA ALA B 5 -5.600 -1.791 0.833 1.00 0.00 BH 47 | ATOM 46 CB ALA B 5 -3.792 -2.416 1.640 1.00 0.00 BH 48 | ATOM 47 HB1 ALA B 5 -3.238 -2.513 0.682 1.00 0.00 BH 49 | ATOM 48 HB2 ALA B 5 -3.051 -2.249 2.451 1.00 0.00 BH 50 | ATOM 49 HB3 ALA B 5 -4.151 -3.455 1.805 1.00 0.00 BH 51 | ATOM 50 C ALA B 5 -5.728 -1.269 2.853 1.00 0.00 BH 52 | ATOM 51 O ALA B 5 -6.821 -1.826 3.026 1.00 0.00 BH 53 | ATOM 52 N ALA B 6 -5.092 -0.721 3.920 1.00 0.00 BH 54 | ATOM 53 HN ALA B 6 -4.250 -0.199 3.808 1.00 0.00 BH 55 | ATOM 54 CA ALA B 6 -5.756 -0.450 5.212 1.00 0.00 BH 56 | ATOM 55 HA ALA B 6 -6.319 -1.344 5.435 1.00 0.00 BH 57 | ATOM 56 CB ALA B 6 -4.701 -0.089 6.243 1.00 0.00 BH 58 | ATOM 57 HB1 ALA B 6 -4.174 0.836 5.923 1.00 0.00 BH 59 | ATOM 58 HB2 ALA B 6 -5.122 -0.006 7.268 1.00 0.00 BH 60 | ATOM 59 HB3 ALA B 6 -4.066 -0.993 6.365 1.00 0.00 BH 61 | ATOM 60 C ALA B 6 -6.839 0.547 5.134 1.00 0.00 BH 62 | ATOM 61 O ALA B 6 -7.796 0.344 5.789 1.00 0.00 BH 63 | ATOM 62 N ALA B 7 -6.709 1.632 4.377 1.00 0.00 BH 64 | ATOM 63 HN ALA B 7 -5.900 1.830 3.830 1.00 0.00 BH 65 | ATOM 64 CA ALA B 7 -7.707 2.606 4.337 1.00 0.00 BH 66 | ATOM 65 HA ALA B 7 -8.028 2.824 5.345 1.00 0.00 BH 67 | ATOM 66 CB ALA B 7 -6.920 3.781 3.934 1.00 0.00 BH 68 | ATOM 67 HB1 ALA B 7 -6.703 3.722 2.846 1.00 0.00 BH 69 | ATOM 68 HB2 ALA B 7 -7.445 4.746 4.096 1.00 0.00 BH 70 | ATOM 69 HB3 ALA B 7 -5.940 3.795 4.458 1.00 0.00 BH 71 | ATOM 70 C ALA B 7 -8.912 2.354 3.463 1.00 0.00 BH 72 | ATOM 71 O ALA B 7 -9.974 2.853 3.663 1.00 0.00 BH 73 | ATOM 72 N ALA B 8 -8.864 1.404 2.514 1.00 0.00 BH 74 | ATOM 73 HN ALA B 8 -7.932 1.244 2.200 1.00 0.00 BH 75 | ATOM 74 CA ALA B 8 -10.008 0.910 1.816 1.00 0.00 BH 76 | ATOM 75 HA ALA B 8 -10.785 1.635 1.621 1.00 0.00 BH 77 | ATOM 76 CB ALA B 8 -9.572 0.291 0.457 1.00 0.00 BH 78 | ATOM 77 HB1 ALA B 8 -10.397 -0.326 0.040 1.00 0.00 BH 79 | ATOM 78 HB2 ALA B 8 -9.311 1.110 -0.247 1.00 0.00 BH 80 | ATOM 79 HB3 ALA B 8 -8.793 -0.479 0.643 1.00 0.00 BH 81 | ATOM 80 C ALA B 8 -10.663 -0.166 2.707 1.00 0.00 BH 82 | ATOM 81 O ALA B 8 -11.882 -0.432 2.666 1.00 0.00 BH 83 | ATOM 82 N ALA B 9 -9.886 -0.789 3.580 1.00 0.00 BH 84 | ATOM 83 HN ALA B 9 -8.904 -0.621 3.609 1.00 0.00 BH 85 | ATOM 84 CA ALA B 9 -10.404 -1.774 4.539 1.00 0.00 BH 86 | ATOM 85 HA ALA B 9 -10.996 -2.532 4.049 1.00 0.00 BH 87 | ATOM 86 CB ALA B 9 -9.238 -2.543 5.191 1.00 0.00 BH 88 | ATOM 87 HB1 ALA B 9 -8.806 -3.097 4.331 1.00 0.00 BH 89 | ATOM 88 HB2 ALA B 9 -8.467 -1.819 5.532 1.00 0.00 BH 90 | ATOM 89 HB3 ALA B 9 -9.463 -3.262 6.007 1.00 0.00 BH 91 | ATOM 90 C ALA B 9 -11.212 -1.063 5.618 1.00 0.00 BH 92 | ATOM 91 O ALA B 9 -12.370 -1.417 5.769 1.00 0.00 BH 93 | ATOM 92 C ALA B 10 -11.957 1.980 7.072 1.00 0.00 BH 94 | ATOM 93 O ALA B 10 -11.964 3.008 7.760 1.00 0.00 BH 95 | ATOM 94 NT ALA B 10 -12.813 1.968 5.971 1.00 0.00 BH 96 | ATOM 95 HT1 ALA B 10 -13.399 2.748 5.755 1.00 0.00 BH 97 | ATOM 96 HT2 ALA B 10 -12.618 1.237 5.316 1.00 0.00 BH 98 | ATOM 97 N ALA B 10 -10.690 0.020 6.213 1.00 0.00 BH 99 | ATOM 98 HN ALA B 10 -9.720 0.133 6.012 1.00 0.00 BH 100 | ATOM 99 CA ALA B 10 -11.166 0.664 7.402 1.00 0.00 BH 101 | ATOM 100 HA ALA B 10 -11.936 0.058 7.856 1.00 0.00 BH 102 | ATOM 101 CB ALA B 10 -10.058 0.920 8.404 1.00 0.00 BH 103 | ATOM 102 HB1 ALA B 10 -9.202 1.387 7.871 1.00 0.00 BH 104 | ATOM 103 HB2 ALA B 10 -10.427 1.550 9.242 1.00 0.00 BH 105 | ATOM 104 HB3 ALA B 10 -9.603 -0.048 8.702 1.00 0.00 BH 106 | END 107 | -------------------------------------------------------------------------------- /Openmm_Plumed/WTM-eABF/deca-ala.psf: -------------------------------------------------------------------------------- 1 | PSF 2 | 3 | 1 !NTITLE 4 | REMARKS original generated structure x-plor psf file 5 | 6 | 104 !NATOM 7 | 1 BH 1 ALA N NH3 -0.620000 14.0070 0 8 | 2 BH 1 ALA HT2 HC 0.310000 1.0080 0 9 | 3 BH 1 ALA HT3 HC 0.310000 1.0080 0 10 | 4 BH 1 ALA CA CT1 -0.100000 12.0110 0 11 | 5 BH 1 ALA HA HB 0.100000 1.0080 0 12 | 6 BH 1 ALA CB CT3 -0.270000 12.0110 0 13 | 7 BH 1 ALA HB1 HA 0.090000 1.0080 0 14 | 8 BH 1 ALA HB2 HA 0.090000 1.0080 0 15 | 9 BH 1 ALA HB3 HA 0.090000 1.0080 0 16 | 10 BH 1 ALA C C 0.510000 12.0110 0 17 | 11 BH 1 ALA O O -0.510000 15.9990 0 18 | 12 BH 2 ALA N NH1 -0.470000 14.0070 0 19 | 13 BH 2 ALA HN H 0.310000 1.0080 0 20 | 14 BH 2 ALA CA CT1 0.070000 12.0110 0 21 | 15 BH 2 ALA HA HB 0.090000 1.0080 0 22 | 16 BH 2 ALA CB CT3 -0.270000 12.0110 0 23 | 17 BH 2 ALA HB1 HA 0.090000 1.0080 0 24 | 18 BH 2 ALA HB2 HA 0.090000 1.0080 0 25 | 19 BH 2 ALA HB3 HA 0.090000 1.0080 0 26 | 20 BH 2 ALA C C 0.510000 12.0110 0 27 | 21 BH 2 ALA O O -0.510000 15.9990 0 28 | 22 BH 3 ALA N NH1 -0.470000 14.0070 0 29 | 23 BH 3 ALA HN H 0.310000 1.0080 0 30 | 24 BH 3 ALA CA CT1 0.070000 12.0110 0 31 | 25 BH 3 ALA HA HB 0.090000 1.0080 0 32 | 26 BH 3 ALA CB CT3 -0.270000 12.0110 0 33 | 27 BH 3 ALA HB1 HA 0.090000 1.0080 0 34 | 28 BH 3 ALA HB2 HA 0.090000 1.0080 0 35 | 29 BH 3 ALA HB3 HA 0.090000 1.0080 0 36 | 30 BH 3 ALA C C 0.510000 12.0110 0 37 | 31 BH 3 ALA O O -0.510000 15.9990 0 38 | 32 BH 4 ALA N NH1 -0.470000 14.0070 0 39 | 33 BH 4 ALA HN H 0.310000 1.0080 0 40 | 34 BH 4 ALA CA CT1 0.070000 12.0110 0 41 | 35 BH 4 ALA HA HB 0.090000 1.0080 0 42 | 36 BH 4 ALA CB CT3 -0.270000 12.0110 0 43 | 37 BH 4 ALA HB1 HA 0.090000 1.0080 0 44 | 38 BH 4 ALA HB2 HA 0.090000 1.0080 0 45 | 39 BH 4 ALA HB3 HA 0.090000 1.0080 0 46 | 40 BH 4 ALA C C 0.510000 12.0110 0 47 | 41 BH 4 ALA O O -0.510000 15.9990 0 48 | 42 BH 5 ALA N NH1 -0.470000 14.0070 0 49 | 43 BH 5 ALA HN H 0.310000 1.0080 0 50 | 44 BH 5 ALA CA CT1 0.070000 12.0110 0 51 | 45 BH 5 ALA HA HB 0.090000 1.0080 0 52 | 46 BH 5 ALA CB CT3 -0.270000 12.0110 0 53 | 47 BH 5 ALA HB1 HA 0.090000 1.0080 0 54 | 48 BH 5 ALA HB2 HA 0.090000 1.0080 0 55 | 49 BH 5 ALA HB3 HA 0.090000 1.0080 0 56 | 50 BH 5 ALA C C 0.510000 12.0110 0 57 | 51 BH 5 ALA O O -0.510000 15.9990 0 58 | 52 BH 6 ALA N NH1 -0.470000 14.0070 0 59 | 53 BH 6 ALA HN H 0.310000 1.0080 0 60 | 54 BH 6 ALA CA CT1 0.070000 12.0110 0 61 | 55 BH 6 ALA HA HB 0.090000 1.0080 0 62 | 56 BH 6 ALA CB CT3 -0.270000 12.0110 0 63 | 57 BH 6 ALA HB1 HA 0.090000 1.0080 0 64 | 58 BH 6 ALA HB2 HA 0.090000 1.0080 0 65 | 59 BH 6 ALA HB3 HA 0.090000 1.0080 0 66 | 60 BH 6 ALA C C 0.510000 12.0110 0 67 | 61 BH 6 ALA O O -0.510000 15.9990 0 68 | 62 BH 7 ALA N NH1 -0.470000 14.0070 0 69 | 63 BH 7 ALA HN H 0.310000 1.0080 0 70 | 64 BH 7 ALA CA CT1 0.070000 12.0110 0 71 | 65 BH 7 ALA HA HB 0.090000 1.0080 0 72 | 66 BH 7 ALA CB CT3 -0.270000 12.0110 0 73 | 67 BH 7 ALA HB1 HA 0.090000 1.0080 0 74 | 68 BH 7 ALA HB2 HA 0.090000 1.0080 0 75 | 69 BH 7 ALA HB3 HA 0.090000 1.0080 0 76 | 70 BH 7 ALA C C 0.510000 12.0110 0 77 | 71 BH 7 ALA O O -0.510000 15.9990 0 78 | 72 BH 8 ALA N NH1 -0.470000 14.0070 0 79 | 73 BH 8 ALA HN H 0.310000 1.0080 0 80 | 74 BH 8 ALA CA CT1 0.070000 12.0110 0 81 | 75 BH 8 ALA HA HB 0.090000 1.0080 0 82 | 76 BH 8 ALA CB CT3 -0.270000 12.0110 0 83 | 77 BH 8 ALA HB1 HA 0.090000 1.0080 0 84 | 78 BH 8 ALA HB2 HA 0.090000 1.0080 0 85 | 79 BH 8 ALA HB3 HA 0.090000 1.0080 0 86 | 80 BH 8 ALA C C 0.510000 12.0110 0 87 | 81 BH 8 ALA O O -0.510000 15.9990 0 88 | 82 BH 9 ALA N NH1 -0.470000 14.0070 0 89 | 83 BH 9 ALA HN H 0.310000 1.0080 0 90 | 84 BH 9 ALA CA CT1 0.070000 12.0110 0 91 | 85 BH 9 ALA HA HB 0.090000 1.0080 0 92 | 86 BH 9 ALA CB CT3 -0.270000 12.0110 0 93 | 87 BH 9 ALA HB1 HA 0.090000 1.0080 0 94 | 88 BH 9 ALA HB2 HA 0.090000 1.0080 0 95 | 89 BH 9 ALA HB3 HA 0.090000 1.0080 0 96 | 90 BH 9 ALA C C 0.510000 12.0110 0 97 | 91 BH 9 ALA O O -0.510000 15.9990 0 98 | 92 BH 10 ALA C CC 0.550000 12.0110 0 99 | 93 BH 10 ALA O O -0.550000 15.9990 0 100 | 94 BH 10 ALA NT NH2 -0.620000 14.0070 0 101 | 95 BH 10 ALA HT1 H 0.320000 1.0080 0 102 | 96 BH 10 ALA HT2 H 0.300000 1.0080 0 103 | 97 BH 10 ALA N NH1 -0.470000 14.0070 0 104 | 98 BH 10 ALA HN H 0.310000 1.0080 0 105 | 99 BH 10 ALA CA CT1 0.070000 12.0110 0 106 | 100 BH 10 ALA HA HB 0.090000 1.0080 0 107 | 101 BH 10 ALA CB CT3 -0.270000 12.0110 0 108 | 102 BH 10 ALA HB1 HA 0.090000 1.0080 0 109 | 103 BH 10 ALA HB2 HA 0.090000 1.0080 0 110 | 104 BH 10 ALA HB3 HA 0.090000 1.0080 0 111 | 112 | 103 !NBOND: bonds 113 | 1 4 2 1 3 1 4 5 114 | 6 4 6 7 6 8 6 9 115 | 10 4 10 12 11 10 12 13 116 | 12 14 14 15 16 14 16 17 117 | 16 18 16 19 20 14 20 22 118 | 21 20 22 23 22 24 24 25 119 | 26 24 26 27 26 28 26 29 120 | 30 24 30 32 31 30 32 33 121 | 32 34 34 35 36 34 36 37 122 | 36 38 36 39 40 34 40 42 123 | 41 40 42 43 42 44 44 45 124 | 46 44 46 47 46 48 46 49 125 | 50 44 50 52 51 50 52 53 126 | 52 54 54 55 56 54 56 57 127 | 56 58 56 59 60 54 60 62 128 | 61 60 62 63 62 64 64 65 129 | 66 64 66 67 66 68 66 69 130 | 70 64 70 72 71 70 72 73 131 | 72 74 74 75 76 74 76 77 132 | 76 78 76 79 80 74 80 82 133 | 81 80 82 83 82 84 84 85 134 | 86 84 86 87 86 88 86 89 135 | 90 84 90 97 91 90 92 94 136 | 92 99 93 92 94 95 94 96 137 | 97 98 97 99 99 100 101 99 138 | 101 102 101 103 101 104 139 | 140 | 183 !NTHETA: angles 141 | 1 4 5 1 4 10 2 1 4 142 | 2 1 3 3 1 4 4 10 11 143 | 4 10 12 4 6 9 4 6 8 144 | 4 6 7 6 4 5 6 4 10 145 | 6 4 1 7 6 9 7 6 8 146 | 8 6 9 10 4 5 12 14 15 147 | 12 14 20 12 10 11 13 12 10 148 | 13 12 14 14 20 21 14 20 22 149 | 14 16 19 14 16 18 14 16 17 150 | 14 12 10 16 14 15 16 14 20 151 | 16 14 12 17 16 19 17 16 18 152 | 18 16 19 20 14 15 22 24 25 153 | 22 24 30 22 20 21 23 22 20 154 | 23 22 24 24 30 31 24 30 32 155 | 24 26 29 24 26 28 24 26 27 156 | 24 22 20 26 24 25 26 24 30 157 | 26 24 22 27 26 29 27 26 28 158 | 28 26 29 30 24 25 32 34 35 159 | 32 34 40 32 30 31 33 32 30 160 | 33 32 34 34 40 41 34 40 42 161 | 34 36 39 34 36 38 34 36 37 162 | 34 32 30 36 34 35 36 34 40 163 | 36 34 32 37 36 39 37 36 38 164 | 38 36 39 40 34 35 42 44 45 165 | 42 44 50 42 40 41 43 42 40 166 | 43 42 44 44 50 51 44 50 52 167 | 44 46 49 44 46 48 44 46 47 168 | 44 42 40 46 44 45 46 44 50 169 | 46 44 42 47 46 49 47 46 48 170 | 48 46 49 50 44 45 52 54 55 171 | 52 54 60 52 50 51 53 52 50 172 | 53 52 54 54 60 61 54 60 62 173 | 54 56 59 54 56 58 54 56 57 174 | 54 52 50 56 54 55 56 54 60 175 | 56 54 52 57 56 59 57 56 58 176 | 58 56 59 60 54 55 62 64 65 177 | 62 64 70 62 60 61 63 62 60 178 | 63 62 64 64 70 71 64 70 72 179 | 64 66 69 64 66 68 64 66 67 180 | 64 62 60 66 64 65 66 64 70 181 | 66 64 62 67 66 69 67 66 68 182 | 68 66 69 70 64 65 72 74 75 183 | 72 74 80 72 70 71 73 72 70 184 | 73 72 74 74 80 81 74 80 82 185 | 74 76 79 74 76 78 74 76 77 186 | 74 72 70 76 74 75 76 74 80 187 | 76 74 72 77 76 79 77 76 78 188 | 78 76 79 80 74 75 82 84 85 189 | 82 84 90 82 80 81 83 82 80 190 | 83 82 84 84 90 91 84 90 97 191 | 84 86 89 84 86 88 84 86 87 192 | 84 82 80 86 84 85 86 84 90 193 | 86 84 82 87 86 89 87 86 88 194 | 88 86 89 90 84 85 92 99 100 195 | 92 94 96 92 94 95 94 92 93 196 | 94 92 99 95 94 96 97 99 100 197 | 97 99 92 97 90 91 98 97 90 198 | 98 97 99 99 101 104 99 101 103 199 | 99 101 102 99 97 90 99 92 93 200 | 101 99 100 101 99 92 101 99 97 201 | 102 101 104 102 101 103 103 101 104 202 | 203 | 251 !NPHI: dihedrals 204 | 1 4 6 7 1 4 6 8 205 | 1 4 6 9 1 4 10 12 206 | 1 4 10 11 2 1 4 6 207 | 2 1 4 10 2 1 4 5 208 | 3 1 4 6 3 1 4 10 209 | 3 1 4 5 4 10 12 13 210 | 4 10 12 14 5 4 6 7 211 | 5 4 6 8 5 4 6 9 212 | 5 4 10 12 5 4 10 11 213 | 6 4 10 12 6 4 10 11 214 | 7 6 4 10 8 6 4 10 215 | 9 6 4 10 10 12 14 16 216 | 10 12 14 20 10 12 14 15 217 | 11 10 12 13 11 10 12 14 218 | 12 14 16 17 12 14 16 18 219 | 12 14 16 19 12 14 20 22 220 | 12 14 20 21 13 12 14 16 221 | 13 12 14 20 13 12 14 15 222 | 14 20 22 23 14 20 22 24 223 | 15 14 16 17 15 14 16 18 224 | 15 14 16 19 15 14 20 22 225 | 15 14 20 21 16 14 20 22 226 | 16 14 20 21 17 16 14 20 227 | 18 16 14 20 19 16 14 20 228 | 20 22 24 26 20 22 24 30 229 | 20 22 24 25 21 20 22 23 230 | 21 20 22 24 22 24 26 27 231 | 22 24 26 28 22 24 26 29 232 | 22 24 30 32 22 24 30 31 233 | 23 22 24 26 23 22 24 30 234 | 23 22 24 25 24 30 32 33 235 | 24 30 32 34 25 24 26 27 236 | 25 24 26 28 25 24 26 29 237 | 25 24 30 32 25 24 30 31 238 | 26 24 30 32 26 24 30 31 239 | 27 26 24 30 28 26 24 30 240 | 29 26 24 30 30 32 34 36 241 | 30 32 34 40 30 32 34 35 242 | 31 30 32 33 31 30 32 34 243 | 32 34 36 37 32 34 36 38 244 | 32 34 36 39 32 34 40 42 245 | 32 34 40 41 33 32 34 36 246 | 33 32 34 40 33 32 34 35 247 | 34 40 42 43 34 40 42 44 248 | 35 34 36 37 35 34 36 38 249 | 35 34 36 39 35 34 40 42 250 | 35 34 40 41 36 34 40 42 251 | 36 34 40 41 37 36 34 40 252 | 38 36 34 40 39 36 34 40 253 | 40 42 44 46 40 42 44 50 254 | 40 42 44 45 41 40 42 43 255 | 41 40 42 44 42 44 46 47 256 | 42 44 46 48 42 44 46 49 257 | 42 44 50 52 42 44 50 51 258 | 43 42 44 46 43 42 44 50 259 | 43 42 44 45 44 50 52 53 260 | 44 50 52 54 45 44 46 47 261 | 45 44 46 48 45 44 46 49 262 | 45 44 50 52 45 44 50 51 263 | 46 44 50 52 46 44 50 51 264 | 47 46 44 50 48 46 44 50 265 | 49 46 44 50 50 52 54 56 266 | 50 52 54 60 50 52 54 55 267 | 51 50 52 53 51 50 52 54 268 | 52 54 56 57 52 54 56 58 269 | 52 54 56 59 52 54 60 62 270 | 52 54 60 61 53 52 54 56 271 | 53 52 54 60 53 52 54 55 272 | 54 60 62 63 54 60 62 64 273 | 55 54 56 57 55 54 56 58 274 | 55 54 56 59 55 54 60 62 275 | 55 54 60 61 56 54 60 62 276 | 56 54 60 61 57 56 54 60 277 | 58 56 54 60 59 56 54 60 278 | 60 62 64 66 60 62 64 70 279 | 60 62 64 65 61 60 62 63 280 | 61 60 62 64 62 64 66 67 281 | 62 64 66 68 62 64 66 69 282 | 62 64 70 72 62 64 70 71 283 | 63 62 64 66 63 62 64 70 284 | 63 62 64 65 64 70 72 73 285 | 64 70 72 74 65 64 66 67 286 | 65 64 66 68 65 64 66 69 287 | 65 64 70 72 65 64 70 71 288 | 66 64 70 72 66 64 70 71 289 | 67 66 64 70 68 66 64 70 290 | 69 66 64 70 70 72 74 76 291 | 70 72 74 80 70 72 74 75 292 | 71 70 72 73 71 70 72 74 293 | 72 74 76 77 72 74 76 78 294 | 72 74 76 79 72 74 80 82 295 | 72 74 80 81 73 72 74 76 296 | 73 72 74 80 73 72 74 75 297 | 74 80 82 83 74 80 82 84 298 | 75 74 76 77 75 74 76 78 299 | 75 74 76 79 75 74 80 82 300 | 75 74 80 81 76 74 80 82 301 | 76 74 80 81 77 76 74 80 302 | 78 76 74 80 79 76 74 80 303 | 80 82 84 86 80 82 84 90 304 | 80 82 84 85 81 80 82 83 305 | 81 80 82 84 82 84 86 87 306 | 82 84 86 88 82 84 86 89 307 | 82 84 90 97 82 84 90 91 308 | 83 82 84 86 83 82 84 90 309 | 83 82 84 85 84 90 97 98 310 | 84 90 97 99 85 84 86 87 311 | 85 84 86 88 85 84 86 89 312 | 85 84 90 97 85 84 90 91 313 | 86 84 90 97 86 84 90 91 314 | 87 86 84 90 88 86 84 90 315 | 89 86 84 90 90 97 99 101 316 | 90 97 99 92 90 97 99 100 317 | 91 90 97 98 91 90 97 99 318 | 92 99 101 102 92 99 101 103 319 | 92 99 101 104 92 99 97 98 320 | 93 92 94 95 93 92 94 96 321 | 93 92 99 101 93 92 99 97 322 | 93 92 99 100 94 92 99 101 323 | 94 92 99 97 94 92 99 100 324 | 95 94 92 99 96 94 92 99 325 | 97 99 101 102 97 99 101 103 326 | 97 99 101 104 98 97 99 101 327 | 98 97 99 100 99 92 94 96 328 | 100 99 101 102 100 99 101 103 329 | 100 99 101 104 330 | 331 | 22 !NIMPHI: impropers 332 | 10 4 12 11 12 10 14 13 333 | 20 14 22 21 22 20 24 23 334 | 30 24 32 31 32 30 34 33 335 | 40 34 42 41 42 40 44 43 336 | 50 44 52 51 52 50 54 53 337 | 60 54 62 61 62 60 64 63 338 | 70 64 72 71 72 70 74 73 339 | 80 74 82 81 82 80 84 83 340 | 90 84 97 91 92 94 99 93 341 | 92 99 94 93 94 92 95 96 342 | 94 92 96 95 97 90 99 98 343 | 344 | 0 !NDON: donors 345 | 346 | 347 | 0 !NACC: acceptors 348 | 349 | 350 | 0 !NNB 351 | 352 | 0 0 0 0 0 0 0 0 353 | 0 0 0 0 0 0 0 0 354 | 0 0 0 0 0 0 0 0 355 | 0 0 0 0 0 0 0 0 356 | 0 0 0 0 0 0 0 0 357 | 0 0 0 0 0 0 0 0 358 | 0 0 0 0 0 0 0 0 359 | 0 0 0 0 0 0 0 0 360 | 0 0 0 0 0 0 0 0 361 | 0 0 0 0 0 0 0 0 362 | 0 0 0 0 0 0 0 0 363 | 0 0 0 0 0 0 0 0 364 | 0 0 0 0 0 0 0 0 365 | 366 | 367 | 1 0 !NGRP 368 | 0 0 0 369 | 370 | -------------------------------------------------------------------------------- /Openmm_Plumed/eABF/abf.py: -------------------------------------------------------------------------------- 1 | from simtk.openmm.app import * 2 | from simtk.openmm import * 3 | from simtk.unit import * 4 | from sys import stdout, exit, stderr 5 | 6 | platform = Platform.getPlatformByName('CPU') 7 | properties = {'Threads': '2'} 8 | 9 | psf = CharmmPsfFile('deca-ala.psf') 10 | pdb = PDBFile('deca-ala.pdb') 11 | params = CharmmParameterSet('top_all22_prot.inp','par_all22_prot.inp') 12 | system = psf.createSystem( 13 | params, 14 | nonbondedCutoff=1.2*nanometer, 15 | switchDistance=1.0*nanometer, 16 | hydrogenMass=1.008*amu) 17 | from openmmplumed import * 18 | import colvars 19 | system.addForce(PlumedForce(colvars.script)) 20 | integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.0005*picoseconds) 21 | simulation = Simulation(psf.topology, system, integrator, platform, properties) 22 | simulation.context.setPositions(pdb.positions) 23 | simulation.minimizeEnergy() 24 | simulation.reporters.append(DCDReporter('output/abf.dcd', 1000)) 25 | simulation.reporters.append(CheckpointReporter('output/abf.chk', 1000)) 26 | simulation.reporters.append(StateDataReporter( 27 | stdout, 28 | 1000, 29 | step=True, 30 | volume=True, 31 | density=True, 32 | potentialEnergy=True, 33 | temperature=True, 34 | speed=True, 35 | remainingTime=True, 36 | totalSteps=20000000)) 37 | simulation.step(20000000) 38 | -------------------------------------------------------------------------------- /Openmm_Plumed/eABF/colvars.py: -------------------------------------------------------------------------------- 1 | script = """ 2 | d1: DISTANCE ATOMS=10,92 3 | 4 | eabf: DRR ARG=d1 FULLSAMPLES=500 FRICTION=1.0 TAU=0.2 TEMP=300 TEXTOUTPUT GRID_MIN=1.2 GRID_MAX=3.2 GRID_SPACING=0.01 OUTPUTFREQ=50000 HISTORYFREQ=50000 OUTPUTPREFIX=output/eabf 5 | 6 | uwall: UPPER_WALLS ARG=eabf.d1_fict AT=3.2 KAPPA=300000 7 | lwall: LOWER_WALLS ARG=eabf.d1_fict AT=1.2 KAPPA=300000 8 | 9 | PRINT STRIDE=10000 ARG=d1 FILE=COLVAR 10 | """ 11 | -------------------------------------------------------------------------------- /Openmm_Plumed/eABF/deca-ala.pdb: -------------------------------------------------------------------------------- 1 | REMARK FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 50000 2 | ATOM 1 N ALA B 1 0.113 -2.288 -1.254 1.00 0.00 BH 3 | ATOM 2 HT2 ALA B 1 -0.779 -1.974 -1.687 1.00 0.00 BH 4 | ATOM 3 HT3 ALA B 1 0.803 -2.829 -1.813 1.00 0.00 BH 5 | ATOM 4 CA ALA B 1 0.767 -1.116 -0.506 1.00 0.00 BH 6 | ATOM 5 HA ALA B 1 1.714 -1.559 -0.234 1.00 0.00 BH 7 | ATOM 6 CB ALA B 1 0.790 0.006 -1.515 1.00 0.00 BH 8 | ATOM 7 HB1 ALA B 1 1.247 0.922 -1.085 1.00 0.00 BH 9 | ATOM 8 HB2 ALA B 1 1.323 -0.411 -2.396 1.00 0.00 BH 10 | ATOM 9 HB3 ALA B 1 -0.176 0.421 -1.873 1.00 0.00 BH 11 | ATOM 10 C ALA B 1 -0.064 -0.634 0.728 1.00 0.00 BH 12 | ATOM 11 O ALA B 1 -1.283 -0.502 0.585 1.00 0.00 BH 13 | ATOM 12 N ALA B 2 0.567 -0.384 1.892 1.00 0.00 BH 14 | ATOM 13 HN ALA B 2 1.558 -0.447 1.979 1.00 0.00 BH 15 | ATOM 14 CA ALA B 2 -0.136 -0.308 3.124 1.00 0.00 BH 16 | ATOM 15 HA ALA B 2 -0.582 -1.269 3.333 1.00 0.00 BH 17 | ATOM 16 CB ALA B 2 0.894 -0.058 4.221 1.00 0.00 BH 18 | ATOM 17 HB1 ALA B 2 0.586 0.170 5.264 1.00 0.00 BH 19 | ATOM 18 HB2 ALA B 2 1.386 -1.043 4.368 1.00 0.00 BH 20 | ATOM 19 HB3 ALA B 2 1.572 0.761 3.896 1.00 0.00 BH 21 | ATOM 20 C ALA B 2 -1.193 0.854 3.162 1.00 0.00 BH 22 | ATOM 21 O ALA B 2 -2.372 0.602 3.566 1.00 0.00 BH 23 | ATOM 22 N ALA B 3 -0.856 2.141 2.875 1.00 0.00 BH 24 | ATOM 23 HN ALA B 3 0.082 2.422 2.689 1.00 0.00 BH 25 | ATOM 24 CA ALA B 3 -1.733 3.280 2.950 1.00 0.00 BH 26 | ATOM 25 HA ALA B 3 -1.997 3.414 3.989 1.00 0.00 BH 27 | ATOM 26 CB ALA B 3 -0.919 4.499 2.477 1.00 0.00 BH 28 | ATOM 27 HB1 ALA B 3 -0.655 4.413 1.401 1.00 0.00 BH 29 | ATOM 28 HB2 ALA B 3 -1.373 5.496 2.661 1.00 0.00 BH 30 | ATOM 29 HB3 ALA B 3 0.046 4.517 3.027 1.00 0.00 BH 31 | ATOM 30 C ALA B 3 -3.066 3.199 2.243 1.00 0.00 BH 32 | ATOM 31 O ALA B 3 -4.119 3.466 2.841 1.00 0.00 BH 33 | ATOM 32 N ALA B 4 -3.071 2.558 1.079 1.00 0.00 BH 34 | ATOM 33 HN ALA B 4 -2.166 2.271 0.776 1.00 0.00 BH 35 | ATOM 34 CA ALA B 4 -4.295 2.275 0.353 1.00 0.00 BH 36 | ATOM 35 HA ALA B 4 -4.896 3.161 0.210 1.00 0.00 BH 37 | ATOM 36 CB ALA B 4 -3.971 1.919 -1.163 1.00 0.00 BH 38 | ATOM 37 HB1 ALA B 4 -3.481 2.802 -1.626 1.00 0.00 BH 39 | ATOM 38 HB2 ALA B 4 -3.239 1.084 -1.214 1.00 0.00 BH 40 | ATOM 39 HB3 ALA B 4 -4.905 1.551 -1.638 1.00 0.00 BH 41 | ATOM 40 C ALA B 4 -5.138 1.148 1.014 1.00 0.00 BH 42 | ATOM 41 O ALA B 4 -6.290 1.290 1.505 1.00 0.00 BH 43 | ATOM 42 N ALA B 5 -4.485 -0.069 0.981 1.00 0.00 BH 44 | ATOM 43 HN ALA B 5 -3.535 -0.144 0.687 1.00 0.00 BH 45 | ATOM 44 CA ALA B 5 -4.953 -1.327 1.563 1.00 0.00 BH 46 | ATOM 45 HA ALA B 5 -5.600 -1.791 0.833 1.00 0.00 BH 47 | ATOM 46 CB ALA B 5 -3.792 -2.416 1.640 1.00 0.00 BH 48 | ATOM 47 HB1 ALA B 5 -3.238 -2.513 0.682 1.00 0.00 BH 49 | ATOM 48 HB2 ALA B 5 -3.051 -2.249 2.451 1.00 0.00 BH 50 | ATOM 49 HB3 ALA B 5 -4.151 -3.455 1.805 1.00 0.00 BH 51 | ATOM 50 C ALA B 5 -5.728 -1.269 2.853 1.00 0.00 BH 52 | ATOM 51 O ALA B 5 -6.821 -1.826 3.026 1.00 0.00 BH 53 | ATOM 52 N ALA B 6 -5.092 -0.721 3.920 1.00 0.00 BH 54 | ATOM 53 HN ALA B 6 -4.250 -0.199 3.808 1.00 0.00 BH 55 | ATOM 54 CA ALA B 6 -5.756 -0.450 5.212 1.00 0.00 BH 56 | ATOM 55 HA ALA B 6 -6.319 -1.344 5.435 1.00 0.00 BH 57 | ATOM 56 CB ALA B 6 -4.701 -0.089 6.243 1.00 0.00 BH 58 | ATOM 57 HB1 ALA B 6 -4.174 0.836 5.923 1.00 0.00 BH 59 | ATOM 58 HB2 ALA B 6 -5.122 -0.006 7.268 1.00 0.00 BH 60 | ATOM 59 HB3 ALA B 6 -4.066 -0.993 6.365 1.00 0.00 BH 61 | ATOM 60 C ALA B 6 -6.839 0.547 5.134 1.00 0.00 BH 62 | ATOM 61 O ALA B 6 -7.796 0.344 5.789 1.00 0.00 BH 63 | ATOM 62 N ALA B 7 -6.709 1.632 4.377 1.00 0.00 BH 64 | ATOM 63 HN ALA B 7 -5.900 1.830 3.830 1.00 0.00 BH 65 | ATOM 64 CA ALA B 7 -7.707 2.606 4.337 1.00 0.00 BH 66 | ATOM 65 HA ALA B 7 -8.028 2.824 5.345 1.00 0.00 BH 67 | ATOM 66 CB ALA B 7 -6.920 3.781 3.934 1.00 0.00 BH 68 | ATOM 67 HB1 ALA B 7 -6.703 3.722 2.846 1.00 0.00 BH 69 | ATOM 68 HB2 ALA B 7 -7.445 4.746 4.096 1.00 0.00 BH 70 | ATOM 69 HB3 ALA B 7 -5.940 3.795 4.458 1.00 0.00 BH 71 | ATOM 70 C ALA B 7 -8.912 2.354 3.463 1.00 0.00 BH 72 | ATOM 71 O ALA B 7 -9.974 2.853 3.663 1.00 0.00 BH 73 | ATOM 72 N ALA B 8 -8.864 1.404 2.514 1.00 0.00 BH 74 | ATOM 73 HN ALA B 8 -7.932 1.244 2.200 1.00 0.00 BH 75 | ATOM 74 CA ALA B 8 -10.008 0.910 1.816 1.00 0.00 BH 76 | ATOM 75 HA ALA B 8 -10.785 1.635 1.621 1.00 0.00 BH 77 | ATOM 76 CB ALA B 8 -9.572 0.291 0.457 1.00 0.00 BH 78 | ATOM 77 HB1 ALA B 8 -10.397 -0.326 0.040 1.00 0.00 BH 79 | ATOM 78 HB2 ALA B 8 -9.311 1.110 -0.247 1.00 0.00 BH 80 | ATOM 79 HB3 ALA B 8 -8.793 -0.479 0.643 1.00 0.00 BH 81 | ATOM 80 C ALA B 8 -10.663 -0.166 2.707 1.00 0.00 BH 82 | ATOM 81 O ALA B 8 -11.882 -0.432 2.666 1.00 0.00 BH 83 | ATOM 82 N ALA B 9 -9.886 -0.789 3.580 1.00 0.00 BH 84 | ATOM 83 HN ALA B 9 -8.904 -0.621 3.609 1.00 0.00 BH 85 | ATOM 84 CA ALA B 9 -10.404 -1.774 4.539 1.00 0.00 BH 86 | ATOM 85 HA ALA B 9 -10.996 -2.532 4.049 1.00 0.00 BH 87 | ATOM 86 CB ALA B 9 -9.238 -2.543 5.191 1.00 0.00 BH 88 | ATOM 87 HB1 ALA B 9 -8.806 -3.097 4.331 1.00 0.00 BH 89 | ATOM 88 HB2 ALA B 9 -8.467 -1.819 5.532 1.00 0.00 BH 90 | ATOM 89 HB3 ALA B 9 -9.463 -3.262 6.007 1.00 0.00 BH 91 | ATOM 90 C ALA B 9 -11.212 -1.063 5.618 1.00 0.00 BH 92 | ATOM 91 O ALA B 9 -12.370 -1.417 5.769 1.00 0.00 BH 93 | ATOM 92 C ALA B 10 -11.957 1.980 7.072 1.00 0.00 BH 94 | ATOM 93 O ALA B 10 -11.964 3.008 7.760 1.00 0.00 BH 95 | ATOM 94 NT ALA B 10 -12.813 1.968 5.971 1.00 0.00 BH 96 | ATOM 95 HT1 ALA B 10 -13.399 2.748 5.755 1.00 0.00 BH 97 | ATOM 96 HT2 ALA B 10 -12.618 1.237 5.316 1.00 0.00 BH 98 | ATOM 97 N ALA B 10 -10.690 0.020 6.213 1.00 0.00 BH 99 | ATOM 98 HN ALA B 10 -9.720 0.133 6.012 1.00 0.00 BH 100 | ATOM 99 CA ALA B 10 -11.166 0.664 7.402 1.00 0.00 BH 101 | ATOM 100 HA ALA B 10 -11.936 0.058 7.856 1.00 0.00 BH 102 | ATOM 101 CB ALA B 10 -10.058 0.920 8.404 1.00 0.00 BH 103 | ATOM 102 HB1 ALA B 10 -9.202 1.387 7.871 1.00 0.00 BH 104 | ATOM 103 HB2 ALA B 10 -10.427 1.550 9.242 1.00 0.00 BH 105 | ATOM 104 HB3 ALA B 10 -9.603 -0.048 8.702 1.00 0.00 BH 106 | END 107 | -------------------------------------------------------------------------------- /Openmm_Plumed/eABF/deca-ala.psf: -------------------------------------------------------------------------------- 1 | PSF 2 | 3 | 1 !NTITLE 4 | REMARKS original generated structure x-plor psf file 5 | 6 | 104 !NATOM 7 | 1 BH 1 ALA N NH3 -0.620000 14.0070 0 8 | 2 BH 1 ALA HT2 HC 0.310000 1.0080 0 9 | 3 BH 1 ALA HT3 HC 0.310000 1.0080 0 10 | 4 BH 1 ALA CA CT1 -0.100000 12.0110 0 11 | 5 BH 1 ALA HA HB 0.100000 1.0080 0 12 | 6 BH 1 ALA CB CT3 -0.270000 12.0110 0 13 | 7 BH 1 ALA HB1 HA 0.090000 1.0080 0 14 | 8 BH 1 ALA HB2 HA 0.090000 1.0080 0 15 | 9 BH 1 ALA HB3 HA 0.090000 1.0080 0 16 | 10 BH 1 ALA C C 0.510000 12.0110 0 17 | 11 BH 1 ALA O O -0.510000 15.9990 0 18 | 12 BH 2 ALA N NH1 -0.470000 14.0070 0 19 | 13 BH 2 ALA HN H 0.310000 1.0080 0 20 | 14 BH 2 ALA CA CT1 0.070000 12.0110 0 21 | 15 BH 2 ALA HA HB 0.090000 1.0080 0 22 | 16 BH 2 ALA CB CT3 -0.270000 12.0110 0 23 | 17 BH 2 ALA HB1 HA 0.090000 1.0080 0 24 | 18 BH 2 ALA HB2 HA 0.090000 1.0080 0 25 | 19 BH 2 ALA HB3 HA 0.090000 1.0080 0 26 | 20 BH 2 ALA C C 0.510000 12.0110 0 27 | 21 BH 2 ALA O O -0.510000 15.9990 0 28 | 22 BH 3 ALA N NH1 -0.470000 14.0070 0 29 | 23 BH 3 ALA HN H 0.310000 1.0080 0 30 | 24 BH 3 ALA CA CT1 0.070000 12.0110 0 31 | 25 BH 3 ALA HA HB 0.090000 1.0080 0 32 | 26 BH 3 ALA CB CT3 -0.270000 12.0110 0 33 | 27 BH 3 ALA HB1 HA 0.090000 1.0080 0 34 | 28 BH 3 ALA HB2 HA 0.090000 1.0080 0 35 | 29 BH 3 ALA HB3 HA 0.090000 1.0080 0 36 | 30 BH 3 ALA C C 0.510000 12.0110 0 37 | 31 BH 3 ALA O O -0.510000 15.9990 0 38 | 32 BH 4 ALA N NH1 -0.470000 14.0070 0 39 | 33 BH 4 ALA HN H 0.310000 1.0080 0 40 | 34 BH 4 ALA CA CT1 0.070000 12.0110 0 41 | 35 BH 4 ALA HA HB 0.090000 1.0080 0 42 | 36 BH 4 ALA CB CT3 -0.270000 12.0110 0 43 | 37 BH 4 ALA HB1 HA 0.090000 1.0080 0 44 | 38 BH 4 ALA HB2 HA 0.090000 1.0080 0 45 | 39 BH 4 ALA HB3 HA 0.090000 1.0080 0 46 | 40 BH 4 ALA C C 0.510000 12.0110 0 47 | 41 BH 4 ALA O O -0.510000 15.9990 0 48 | 42 BH 5 ALA N NH1 -0.470000 14.0070 0 49 | 43 BH 5 ALA HN H 0.310000 1.0080 0 50 | 44 BH 5 ALA CA CT1 0.070000 12.0110 0 51 | 45 BH 5 ALA HA HB 0.090000 1.0080 0 52 | 46 BH 5 ALA CB CT3 -0.270000 12.0110 0 53 | 47 BH 5 ALA HB1 HA 0.090000 1.0080 0 54 | 48 BH 5 ALA HB2 HA 0.090000 1.0080 0 55 | 49 BH 5 ALA HB3 HA 0.090000 1.0080 0 56 | 50 BH 5 ALA C C 0.510000 12.0110 0 57 | 51 BH 5 ALA O O -0.510000 15.9990 0 58 | 52 BH 6 ALA N NH1 -0.470000 14.0070 0 59 | 53 BH 6 ALA HN H 0.310000 1.0080 0 60 | 54 BH 6 ALA CA CT1 0.070000 12.0110 0 61 | 55 BH 6 ALA HA HB 0.090000 1.0080 0 62 | 56 BH 6 ALA CB CT3 -0.270000 12.0110 0 63 | 57 BH 6 ALA HB1 HA 0.090000 1.0080 0 64 | 58 BH 6 ALA HB2 HA 0.090000 1.0080 0 65 | 59 BH 6 ALA HB3 HA 0.090000 1.0080 0 66 | 60 BH 6 ALA C C 0.510000 12.0110 0 67 | 61 BH 6 ALA O O -0.510000 15.9990 0 68 | 62 BH 7 ALA N NH1 -0.470000 14.0070 0 69 | 63 BH 7 ALA HN H 0.310000 1.0080 0 70 | 64 BH 7 ALA CA CT1 0.070000 12.0110 0 71 | 65 BH 7 ALA HA HB 0.090000 1.0080 0 72 | 66 BH 7 ALA CB CT3 -0.270000 12.0110 0 73 | 67 BH 7 ALA HB1 HA 0.090000 1.0080 0 74 | 68 BH 7 ALA HB2 HA 0.090000 1.0080 0 75 | 69 BH 7 ALA HB3 HA 0.090000 1.0080 0 76 | 70 BH 7 ALA C C 0.510000 12.0110 0 77 | 71 BH 7 ALA O O -0.510000 15.9990 0 78 | 72 BH 8 ALA N NH1 -0.470000 14.0070 0 79 | 73 BH 8 ALA HN H 0.310000 1.0080 0 80 | 74 BH 8 ALA CA CT1 0.070000 12.0110 0 81 | 75 BH 8 ALA HA HB 0.090000 1.0080 0 82 | 76 BH 8 ALA CB CT3 -0.270000 12.0110 0 83 | 77 BH 8 ALA HB1 HA 0.090000 1.0080 0 84 | 78 BH 8 ALA HB2 HA 0.090000 1.0080 0 85 | 79 BH 8 ALA HB3 HA 0.090000 1.0080 0 86 | 80 BH 8 ALA C C 0.510000 12.0110 0 87 | 81 BH 8 ALA O O -0.510000 15.9990 0 88 | 82 BH 9 ALA N NH1 -0.470000 14.0070 0 89 | 83 BH 9 ALA HN H 0.310000 1.0080 0 90 | 84 BH 9 ALA CA CT1 0.070000 12.0110 0 91 | 85 BH 9 ALA HA HB 0.090000 1.0080 0 92 | 86 BH 9 ALA CB CT3 -0.270000 12.0110 0 93 | 87 BH 9 ALA HB1 HA 0.090000 1.0080 0 94 | 88 BH 9 ALA HB2 HA 0.090000 1.0080 0 95 | 89 BH 9 ALA HB3 HA 0.090000 1.0080 0 96 | 90 BH 9 ALA C C 0.510000 12.0110 0 97 | 91 BH 9 ALA O O -0.510000 15.9990 0 98 | 92 BH 10 ALA C CC 0.550000 12.0110 0 99 | 93 BH 10 ALA O O -0.550000 15.9990 0 100 | 94 BH 10 ALA NT NH2 -0.620000 14.0070 0 101 | 95 BH 10 ALA HT1 H 0.320000 1.0080 0 102 | 96 BH 10 ALA HT2 H 0.300000 1.0080 0 103 | 97 BH 10 ALA N NH1 -0.470000 14.0070 0 104 | 98 BH 10 ALA HN H 0.310000 1.0080 0 105 | 99 BH 10 ALA CA CT1 0.070000 12.0110 0 106 | 100 BH 10 ALA HA HB 0.090000 1.0080 0 107 | 101 BH 10 ALA CB CT3 -0.270000 12.0110 0 108 | 102 BH 10 ALA HB1 HA 0.090000 1.0080 0 109 | 103 BH 10 ALA HB2 HA 0.090000 1.0080 0 110 | 104 BH 10 ALA HB3 HA 0.090000 1.0080 0 111 | 112 | 103 !NBOND: bonds 113 | 1 4 2 1 3 1 4 5 114 | 6 4 6 7 6 8 6 9 115 | 10 4 10 12 11 10 12 13 116 | 12 14 14 15 16 14 16 17 117 | 16 18 16 19 20 14 20 22 118 | 21 20 22 23 22 24 24 25 119 | 26 24 26 27 26 28 26 29 120 | 30 24 30 32 31 30 32 33 121 | 32 34 34 35 36 34 36 37 122 | 36 38 36 39 40 34 40 42 123 | 41 40 42 43 42 44 44 45 124 | 46 44 46 47 46 48 46 49 125 | 50 44 50 52 51 50 52 53 126 | 52 54 54 55 56 54 56 57 127 | 56 58 56 59 60 54 60 62 128 | 61 60 62 63 62 64 64 65 129 | 66 64 66 67 66 68 66 69 130 | 70 64 70 72 71 70 72 73 131 | 72 74 74 75 76 74 76 77 132 | 76 78 76 79 80 74 80 82 133 | 81 80 82 83 82 84 84 85 134 | 86 84 86 87 86 88 86 89 135 | 90 84 90 97 91 90 92 94 136 | 92 99 93 92 94 95 94 96 137 | 97 98 97 99 99 100 101 99 138 | 101 102 101 103 101 104 139 | 140 | 183 !NTHETA: angles 141 | 1 4 5 1 4 10 2 1 4 142 | 2 1 3 3 1 4 4 10 11 143 | 4 10 12 4 6 9 4 6 8 144 | 4 6 7 6 4 5 6 4 10 145 | 6 4 1 7 6 9 7 6 8 146 | 8 6 9 10 4 5 12 14 15 147 | 12 14 20 12 10 11 13 12 10 148 | 13 12 14 14 20 21 14 20 22 149 | 14 16 19 14 16 18 14 16 17 150 | 14 12 10 16 14 15 16 14 20 151 | 16 14 12 17 16 19 17 16 18 152 | 18 16 19 20 14 15 22 24 25 153 | 22 24 30 22 20 21 23 22 20 154 | 23 22 24 24 30 31 24 30 32 155 | 24 26 29 24 26 28 24 26 27 156 | 24 22 20 26 24 25 26 24 30 157 | 26 24 22 27 26 29 27 26 28 158 | 28 26 29 30 24 25 32 34 35 159 | 32 34 40 32 30 31 33 32 30 160 | 33 32 34 34 40 41 34 40 42 161 | 34 36 39 34 36 38 34 36 37 162 | 34 32 30 36 34 35 36 34 40 163 | 36 34 32 37 36 39 37 36 38 164 | 38 36 39 40 34 35 42 44 45 165 | 42 44 50 42 40 41 43 42 40 166 | 43 42 44 44 50 51 44 50 52 167 | 44 46 49 44 46 48 44 46 47 168 | 44 42 40 46 44 45 46 44 50 169 | 46 44 42 47 46 49 47 46 48 170 | 48 46 49 50 44 45 52 54 55 171 | 52 54 60 52 50 51 53 52 50 172 | 53 52 54 54 60 61 54 60 62 173 | 54 56 59 54 56 58 54 56 57 174 | 54 52 50 56 54 55 56 54 60 175 | 56 54 52 57 56 59 57 56 58 176 | 58 56 59 60 54 55 62 64 65 177 | 62 64 70 62 60 61 63 62 60 178 | 63 62 64 64 70 71 64 70 72 179 | 64 66 69 64 66 68 64 66 67 180 | 64 62 60 66 64 65 66 64 70 181 | 66 64 62 67 66 69 67 66 68 182 | 68 66 69 70 64 65 72 74 75 183 | 72 74 80 72 70 71 73 72 70 184 | 73 72 74 74 80 81 74 80 82 185 | 74 76 79 74 76 78 74 76 77 186 | 74 72 70 76 74 75 76 74 80 187 | 76 74 72 77 76 79 77 76 78 188 | 78 76 79 80 74 75 82 84 85 189 | 82 84 90 82 80 81 83 82 80 190 | 83 82 84 84 90 91 84 90 97 191 | 84 86 89 84 86 88 84 86 87 192 | 84 82 80 86 84 85 86 84 90 193 | 86 84 82 87 86 89 87 86 88 194 | 88 86 89 90 84 85 92 99 100 195 | 92 94 96 92 94 95 94 92 93 196 | 94 92 99 95 94 96 97 99 100 197 | 97 99 92 97 90 91 98 97 90 198 | 98 97 99 99 101 104 99 101 103 199 | 99 101 102 99 97 90 99 92 93 200 | 101 99 100 101 99 92 101 99 97 201 | 102 101 104 102 101 103 103 101 104 202 | 203 | 251 !NPHI: dihedrals 204 | 1 4 6 7 1 4 6 8 205 | 1 4 6 9 1 4 10 12 206 | 1 4 10 11 2 1 4 6 207 | 2 1 4 10 2 1 4 5 208 | 3 1 4 6 3 1 4 10 209 | 3 1 4 5 4 10 12 13 210 | 4 10 12 14 5 4 6 7 211 | 5 4 6 8 5 4 6 9 212 | 5 4 10 12 5 4 10 11 213 | 6 4 10 12 6 4 10 11 214 | 7 6 4 10 8 6 4 10 215 | 9 6 4 10 10 12 14 16 216 | 10 12 14 20 10 12 14 15 217 | 11 10 12 13 11 10 12 14 218 | 12 14 16 17 12 14 16 18 219 | 12 14 16 19 12 14 20 22 220 | 12 14 20 21 13 12 14 16 221 | 13 12 14 20 13 12 14 15 222 | 14 20 22 23 14 20 22 24 223 | 15 14 16 17 15 14 16 18 224 | 15 14 16 19 15 14 20 22 225 | 15 14 20 21 16 14 20 22 226 | 16 14 20 21 17 16 14 20 227 | 18 16 14 20 19 16 14 20 228 | 20 22 24 26 20 22 24 30 229 | 20 22 24 25 21 20 22 23 230 | 21 20 22 24 22 24 26 27 231 | 22 24 26 28 22 24 26 29 232 | 22 24 30 32 22 24 30 31 233 | 23 22 24 26 23 22 24 30 234 | 23 22 24 25 24 30 32 33 235 | 24 30 32 34 25 24 26 27 236 | 25 24 26 28 25 24 26 29 237 | 25 24 30 32 25 24 30 31 238 | 26 24 30 32 26 24 30 31 239 | 27 26 24 30 28 26 24 30 240 | 29 26 24 30 30 32 34 36 241 | 30 32 34 40 30 32 34 35 242 | 31 30 32 33 31 30 32 34 243 | 32 34 36 37 32 34 36 38 244 | 32 34 36 39 32 34 40 42 245 | 32 34 40 41 33 32 34 36 246 | 33 32 34 40 33 32 34 35 247 | 34 40 42 43 34 40 42 44 248 | 35 34 36 37 35 34 36 38 249 | 35 34 36 39 35 34 40 42 250 | 35 34 40 41 36 34 40 42 251 | 36 34 40 41 37 36 34 40 252 | 38 36 34 40 39 36 34 40 253 | 40 42 44 46 40 42 44 50 254 | 40 42 44 45 41 40 42 43 255 | 41 40 42 44 42 44 46 47 256 | 42 44 46 48 42 44 46 49 257 | 42 44 50 52 42 44 50 51 258 | 43 42 44 46 43 42 44 50 259 | 43 42 44 45 44 50 52 53 260 | 44 50 52 54 45 44 46 47 261 | 45 44 46 48 45 44 46 49 262 | 45 44 50 52 45 44 50 51 263 | 46 44 50 52 46 44 50 51 264 | 47 46 44 50 48 46 44 50 265 | 49 46 44 50 50 52 54 56 266 | 50 52 54 60 50 52 54 55 267 | 51 50 52 53 51 50 52 54 268 | 52 54 56 57 52 54 56 58 269 | 52 54 56 59 52 54 60 62 270 | 52 54 60 61 53 52 54 56 271 | 53 52 54 60 53 52 54 55 272 | 54 60 62 63 54 60 62 64 273 | 55 54 56 57 55 54 56 58 274 | 55 54 56 59 55 54 60 62 275 | 55 54 60 61 56 54 60 62 276 | 56 54 60 61 57 56 54 60 277 | 58 56 54 60 59 56 54 60 278 | 60 62 64 66 60 62 64 70 279 | 60 62 64 65 61 60 62 63 280 | 61 60 62 64 62 64 66 67 281 | 62 64 66 68 62 64 66 69 282 | 62 64 70 72 62 64 70 71 283 | 63 62 64 66 63 62 64 70 284 | 63 62 64 65 64 70 72 73 285 | 64 70 72 74 65 64 66 67 286 | 65 64 66 68 65 64 66 69 287 | 65 64 70 72 65 64 70 71 288 | 66 64 70 72 66 64 70 71 289 | 67 66 64 70 68 66 64 70 290 | 69 66 64 70 70 72 74 76 291 | 70 72 74 80 70 72 74 75 292 | 71 70 72 73 71 70 72 74 293 | 72 74 76 77 72 74 76 78 294 | 72 74 76 79 72 74 80 82 295 | 72 74 80 81 73 72 74 76 296 | 73 72 74 80 73 72 74 75 297 | 74 80 82 83 74 80 82 84 298 | 75 74 76 77 75 74 76 78 299 | 75 74 76 79 75 74 80 82 300 | 75 74 80 81 76 74 80 82 301 | 76 74 80 81 77 76 74 80 302 | 78 76 74 80 79 76 74 80 303 | 80 82 84 86 80 82 84 90 304 | 80 82 84 85 81 80 82 83 305 | 81 80 82 84 82 84 86 87 306 | 82 84 86 88 82 84 86 89 307 | 82 84 90 97 82 84 90 91 308 | 83 82 84 86 83 82 84 90 309 | 83 82 84 85 84 90 97 98 310 | 84 90 97 99 85 84 86 87 311 | 85 84 86 88 85 84 86 89 312 | 85 84 90 97 85 84 90 91 313 | 86 84 90 97 86 84 90 91 314 | 87 86 84 90 88 86 84 90 315 | 89 86 84 90 90 97 99 101 316 | 90 97 99 92 90 97 99 100 317 | 91 90 97 98 91 90 97 99 318 | 92 99 101 102 92 99 101 103 319 | 92 99 101 104 92 99 97 98 320 | 93 92 94 95 93 92 94 96 321 | 93 92 99 101 93 92 99 97 322 | 93 92 99 100 94 92 99 101 323 | 94 92 99 97 94 92 99 100 324 | 95 94 92 99 96 94 92 99 325 | 97 99 101 102 97 99 101 103 326 | 97 99 101 104 98 97 99 101 327 | 98 97 99 100 99 92 94 96 328 | 100 99 101 102 100 99 101 103 329 | 100 99 101 104 330 | 331 | 22 !NIMPHI: impropers 332 | 10 4 12 11 12 10 14 13 333 | 20 14 22 21 22 20 24 23 334 | 30 24 32 31 32 30 34 33 335 | 40 34 42 41 42 40 44 43 336 | 50 44 52 51 52 50 54 53 337 | 60 54 62 61 62 60 64 63 338 | 70 64 72 71 72 70 74 73 339 | 80 74 82 81 82 80 84 83 340 | 90 84 97 91 92 94 99 93 341 | 92 99 94 93 94 92 95 96 342 | 94 92 96 95 97 90 99 98 343 | 344 | 0 !NDON: donors 345 | 346 | 347 | 0 !NACC: acceptors 348 | 349 | 350 | 0 !NNB 351 | 352 | 0 0 0 0 0 0 0 0 353 | 0 0 0 0 0 0 0 0 354 | 0 0 0 0 0 0 0 0 355 | 0 0 0 0 0 0 0 0 356 | 0 0 0 0 0 0 0 0 357 | 0 0 0 0 0 0 0 0 358 | 0 0 0 0 0 0 0 0 359 | 0 0 0 0 0 0 0 0 360 | 0 0 0 0 0 0 0 0 361 | 0 0 0 0 0 0 0 0 362 | 0 0 0 0 0 0 0 0 363 | 0 0 0 0 0 0 0 0 364 | 0 0 0 0 0 0 0 0 365 | 366 | 367 | 1 0 !NGRP 368 | 0 0 0 369 | 370 | -------------------------------------------------------------------------------- /Openmm_Plumed/meta-eABF/abf.py: -------------------------------------------------------------------------------- 1 | from simtk.openmm.app import * 2 | from simtk.openmm import * 3 | from simtk.unit import * 4 | from sys import stdout, exit, stderr 5 | 6 | platform = Platform.getPlatformByName('CPU') 7 | properties = {'Threads': '2'} 8 | 9 | psf = CharmmPsfFile('deca-ala.psf') 10 | pdb = PDBFile('deca-ala.pdb') 11 | params = CharmmParameterSet('top_all22_prot.inp','par_all22_prot.inp') 12 | system = psf.createSystem( 13 | params, 14 | nonbondedCutoff=1.2*nanometer, 15 | switchDistance=1.0*nanometer, 16 | hydrogenMass=1.008*amu) 17 | from openmmplumed import * 18 | import colvars 19 | system.addForce(PlumedForce(colvars.script)) 20 | integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.0005*picoseconds) 21 | simulation = Simulation(psf.topology, system, integrator, platform, properties) 22 | simulation.context.setPositions(pdb.positions) 23 | simulation.minimizeEnergy() 24 | simulation.reporters.append(DCDReporter('output/abf.dcd', 1000)) 25 | simulation.reporters.append(CheckpointReporter('output/abf.chk', 1000)) 26 | simulation.reporters.append(StateDataReporter( 27 | stdout, 28 | 1000, 29 | step=True, 30 | volume=True, 31 | density=True, 32 | potentialEnergy=True, 33 | temperature=True, 34 | speed=True, 35 | remainingTime=True, 36 | totalSteps=20000000)) 37 | simulation.step(20000000) 38 | -------------------------------------------------------------------------------- /Openmm_Plumed/meta-eABF/colvars.py: -------------------------------------------------------------------------------- 1 | script = """ 2 | d1: DISTANCE ATOMS=10,92 3 | 4 | eabf: DRR ARG=d1 FULLSAMPLES=500 FRICTION=1.0 TAU=0.2 TEMP=300 TEXTOUTPUT GRID_MIN=1.2 GRID_MAX=3.2 GRID_SPACING=0.01 OUTPUTFREQ=50000 HISTORYFREQ=50000 OUTPUTPREFIX=output/eabf 5 | wtmeabf: METAD ARG=eabf.d1_fict PACE=1000 SIGMA=0.25 HEIGHT=0.4 GRID_MIN=0.7 GRID_MAX=3.7 6 | 7 | uwall: UPPER_WALLS ARG=eabf.d1_fict AT=3.2 KAPPA=300000 8 | lwall: LOWER_WALLS ARG=eabf.d1_fict AT=1.2 KAPPA=300000 9 | 10 | PRINT STRIDE=10000 ARG=d1 FILE=COLVAR 11 | """ 12 | -------------------------------------------------------------------------------- /Openmm_Plumed/meta-eABF/deca-ala.pdb: -------------------------------------------------------------------------------- 1 | REMARK FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 50000 2 | ATOM 1 N ALA B 1 0.113 -2.288 -1.254 1.00 0.00 BH 3 | ATOM 2 HT2 ALA B 1 -0.779 -1.974 -1.687 1.00 0.00 BH 4 | ATOM 3 HT3 ALA B 1 0.803 -2.829 -1.813 1.00 0.00 BH 5 | ATOM 4 CA ALA B 1 0.767 -1.116 -0.506 1.00 0.00 BH 6 | ATOM 5 HA ALA B 1 1.714 -1.559 -0.234 1.00 0.00 BH 7 | ATOM 6 CB ALA B 1 0.790 0.006 -1.515 1.00 0.00 BH 8 | ATOM 7 HB1 ALA B 1 1.247 0.922 -1.085 1.00 0.00 BH 9 | ATOM 8 HB2 ALA B 1 1.323 -0.411 -2.396 1.00 0.00 BH 10 | ATOM 9 HB3 ALA B 1 -0.176 0.421 -1.873 1.00 0.00 BH 11 | ATOM 10 C ALA B 1 -0.064 -0.634 0.728 1.00 0.00 BH 12 | ATOM 11 O ALA B 1 -1.283 -0.502 0.585 1.00 0.00 BH 13 | ATOM 12 N ALA B 2 0.567 -0.384 1.892 1.00 0.00 BH 14 | ATOM 13 HN ALA B 2 1.558 -0.447 1.979 1.00 0.00 BH 15 | ATOM 14 CA ALA B 2 -0.136 -0.308 3.124 1.00 0.00 BH 16 | ATOM 15 HA ALA B 2 -0.582 -1.269 3.333 1.00 0.00 BH 17 | ATOM 16 CB ALA B 2 0.894 -0.058 4.221 1.00 0.00 BH 18 | ATOM 17 HB1 ALA B 2 0.586 0.170 5.264 1.00 0.00 BH 19 | ATOM 18 HB2 ALA B 2 1.386 -1.043 4.368 1.00 0.00 BH 20 | ATOM 19 HB3 ALA B 2 1.572 0.761 3.896 1.00 0.00 BH 21 | ATOM 20 C ALA B 2 -1.193 0.854 3.162 1.00 0.00 BH 22 | ATOM 21 O ALA B 2 -2.372 0.602 3.566 1.00 0.00 BH 23 | ATOM 22 N ALA B 3 -0.856 2.141 2.875 1.00 0.00 BH 24 | ATOM 23 HN ALA B 3 0.082 2.422 2.689 1.00 0.00 BH 25 | ATOM 24 CA ALA B 3 -1.733 3.280 2.950 1.00 0.00 BH 26 | ATOM 25 HA ALA B 3 -1.997 3.414 3.989 1.00 0.00 BH 27 | ATOM 26 CB ALA B 3 -0.919 4.499 2.477 1.00 0.00 BH 28 | ATOM 27 HB1 ALA B 3 -0.655 4.413 1.401 1.00 0.00 BH 29 | ATOM 28 HB2 ALA B 3 -1.373 5.496 2.661 1.00 0.00 BH 30 | ATOM 29 HB3 ALA B 3 0.046 4.517 3.027 1.00 0.00 BH 31 | ATOM 30 C ALA B 3 -3.066 3.199 2.243 1.00 0.00 BH 32 | ATOM 31 O ALA B 3 -4.119 3.466 2.841 1.00 0.00 BH 33 | ATOM 32 N ALA B 4 -3.071 2.558 1.079 1.00 0.00 BH 34 | ATOM 33 HN ALA B 4 -2.166 2.271 0.776 1.00 0.00 BH 35 | ATOM 34 CA ALA B 4 -4.295 2.275 0.353 1.00 0.00 BH 36 | ATOM 35 HA ALA B 4 -4.896 3.161 0.210 1.00 0.00 BH 37 | ATOM 36 CB ALA B 4 -3.971 1.919 -1.163 1.00 0.00 BH 38 | ATOM 37 HB1 ALA B 4 -3.481 2.802 -1.626 1.00 0.00 BH 39 | ATOM 38 HB2 ALA B 4 -3.239 1.084 -1.214 1.00 0.00 BH 40 | ATOM 39 HB3 ALA B 4 -4.905 1.551 -1.638 1.00 0.00 BH 41 | ATOM 40 C ALA B 4 -5.138 1.148 1.014 1.00 0.00 BH 42 | ATOM 41 O ALA B 4 -6.290 1.290 1.505 1.00 0.00 BH 43 | ATOM 42 N ALA B 5 -4.485 -0.069 0.981 1.00 0.00 BH 44 | ATOM 43 HN ALA B 5 -3.535 -0.144 0.687 1.00 0.00 BH 45 | ATOM 44 CA ALA B 5 -4.953 -1.327 1.563 1.00 0.00 BH 46 | ATOM 45 HA ALA B 5 -5.600 -1.791 0.833 1.00 0.00 BH 47 | ATOM 46 CB ALA B 5 -3.792 -2.416 1.640 1.00 0.00 BH 48 | ATOM 47 HB1 ALA B 5 -3.238 -2.513 0.682 1.00 0.00 BH 49 | ATOM 48 HB2 ALA B 5 -3.051 -2.249 2.451 1.00 0.00 BH 50 | ATOM 49 HB3 ALA B 5 -4.151 -3.455 1.805 1.00 0.00 BH 51 | ATOM 50 C ALA B 5 -5.728 -1.269 2.853 1.00 0.00 BH 52 | ATOM 51 O ALA B 5 -6.821 -1.826 3.026 1.00 0.00 BH 53 | ATOM 52 N ALA B 6 -5.092 -0.721 3.920 1.00 0.00 BH 54 | ATOM 53 HN ALA B 6 -4.250 -0.199 3.808 1.00 0.00 BH 55 | ATOM 54 CA ALA B 6 -5.756 -0.450 5.212 1.00 0.00 BH 56 | ATOM 55 HA ALA B 6 -6.319 -1.344 5.435 1.00 0.00 BH 57 | ATOM 56 CB ALA B 6 -4.701 -0.089 6.243 1.00 0.00 BH 58 | ATOM 57 HB1 ALA B 6 -4.174 0.836 5.923 1.00 0.00 BH 59 | ATOM 58 HB2 ALA B 6 -5.122 -0.006 7.268 1.00 0.00 BH 60 | ATOM 59 HB3 ALA B 6 -4.066 -0.993 6.365 1.00 0.00 BH 61 | ATOM 60 C ALA B 6 -6.839 0.547 5.134 1.00 0.00 BH 62 | ATOM 61 O ALA B 6 -7.796 0.344 5.789 1.00 0.00 BH 63 | ATOM 62 N ALA B 7 -6.709 1.632 4.377 1.00 0.00 BH 64 | ATOM 63 HN ALA B 7 -5.900 1.830 3.830 1.00 0.00 BH 65 | ATOM 64 CA ALA B 7 -7.707 2.606 4.337 1.00 0.00 BH 66 | ATOM 65 HA ALA B 7 -8.028 2.824 5.345 1.00 0.00 BH 67 | ATOM 66 CB ALA B 7 -6.920 3.781 3.934 1.00 0.00 BH 68 | ATOM 67 HB1 ALA B 7 -6.703 3.722 2.846 1.00 0.00 BH 69 | ATOM 68 HB2 ALA B 7 -7.445 4.746 4.096 1.00 0.00 BH 70 | ATOM 69 HB3 ALA B 7 -5.940 3.795 4.458 1.00 0.00 BH 71 | ATOM 70 C ALA B 7 -8.912 2.354 3.463 1.00 0.00 BH 72 | ATOM 71 O ALA B 7 -9.974 2.853 3.663 1.00 0.00 BH 73 | ATOM 72 N ALA B 8 -8.864 1.404 2.514 1.00 0.00 BH 74 | ATOM 73 HN ALA B 8 -7.932 1.244 2.200 1.00 0.00 BH 75 | ATOM 74 CA ALA B 8 -10.008 0.910 1.816 1.00 0.00 BH 76 | ATOM 75 HA ALA B 8 -10.785 1.635 1.621 1.00 0.00 BH 77 | ATOM 76 CB ALA B 8 -9.572 0.291 0.457 1.00 0.00 BH 78 | ATOM 77 HB1 ALA B 8 -10.397 -0.326 0.040 1.00 0.00 BH 79 | ATOM 78 HB2 ALA B 8 -9.311 1.110 -0.247 1.00 0.00 BH 80 | ATOM 79 HB3 ALA B 8 -8.793 -0.479 0.643 1.00 0.00 BH 81 | ATOM 80 C ALA B 8 -10.663 -0.166 2.707 1.00 0.00 BH 82 | ATOM 81 O ALA B 8 -11.882 -0.432 2.666 1.00 0.00 BH 83 | ATOM 82 N ALA B 9 -9.886 -0.789 3.580 1.00 0.00 BH 84 | ATOM 83 HN ALA B 9 -8.904 -0.621 3.609 1.00 0.00 BH 85 | ATOM 84 CA ALA B 9 -10.404 -1.774 4.539 1.00 0.00 BH 86 | ATOM 85 HA ALA B 9 -10.996 -2.532 4.049 1.00 0.00 BH 87 | ATOM 86 CB ALA B 9 -9.238 -2.543 5.191 1.00 0.00 BH 88 | ATOM 87 HB1 ALA B 9 -8.806 -3.097 4.331 1.00 0.00 BH 89 | ATOM 88 HB2 ALA B 9 -8.467 -1.819 5.532 1.00 0.00 BH 90 | ATOM 89 HB3 ALA B 9 -9.463 -3.262 6.007 1.00 0.00 BH 91 | ATOM 90 C ALA B 9 -11.212 -1.063 5.618 1.00 0.00 BH 92 | ATOM 91 O ALA B 9 -12.370 -1.417 5.769 1.00 0.00 BH 93 | ATOM 92 C ALA B 10 -11.957 1.980 7.072 1.00 0.00 BH 94 | ATOM 93 O ALA B 10 -11.964 3.008 7.760 1.00 0.00 BH 95 | ATOM 94 NT ALA B 10 -12.813 1.968 5.971 1.00 0.00 BH 96 | ATOM 95 HT1 ALA B 10 -13.399 2.748 5.755 1.00 0.00 BH 97 | ATOM 96 HT2 ALA B 10 -12.618 1.237 5.316 1.00 0.00 BH 98 | ATOM 97 N ALA B 10 -10.690 0.020 6.213 1.00 0.00 BH 99 | ATOM 98 HN ALA B 10 -9.720 0.133 6.012 1.00 0.00 BH 100 | ATOM 99 CA ALA B 10 -11.166 0.664 7.402 1.00 0.00 BH 101 | ATOM 100 HA ALA B 10 -11.936 0.058 7.856 1.00 0.00 BH 102 | ATOM 101 CB ALA B 10 -10.058 0.920 8.404 1.00 0.00 BH 103 | ATOM 102 HB1 ALA B 10 -9.202 1.387 7.871 1.00 0.00 BH 104 | ATOM 103 HB2 ALA B 10 -10.427 1.550 9.242 1.00 0.00 BH 105 | ATOM 104 HB3 ALA B 10 -9.603 -0.048 8.702 1.00 0.00 BH 106 | END 107 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # ABF example files for NAMD and OpenMM 2 | 3 | Example files for running ABF/eABF/meta-eABF/WTM-eABF in NAMD and OpenMM through the Colvars and Plumed free-energy calculation engine. 4 | 5 | Contact fhh2626@gmail.com if there is any problem. 6 | --------------------------------------------------------------------------------