├── .gitignore ├── BF4.zmat ├── Br.zmat ├── CCN3.xyz ├── Cl.zmat ├── LICENSE ├── N1110.zmat ├── N1111.zmat ├── N2220.xyz ├── N2222.xyz ├── N4444.xyz ├── Na.zmat ├── P1111.zmat ├── P1112O2.xyz ├── P111i4.xyz ├── P4444.xyz ├── P66614.zmat ├── PF6.zmat ├── README.md ├── SCN.zmat ├── benzc1im.zmat ├── beti.zmat ├── c12c1im.zmat ├── c1SO3.zmat ├── c1SO4.zmat ├── c1c1im.zmat ├── c1c1pyrr.zmat ├── c2OHc1im.zmat ├── c2SO3.zmat ├── c2SO4.zmat ├── c2c1c1im.zmat ├── c2c1im.zmat ├── c2im.zmat ├── c2o1mpyr.xyz ├── c2py.xyz ├── c3c1im.zmat ├── c3c1pyrr.zmat ├── c4c1c1im.zmat ├── c4c1im.zmat ├── c4c1pyrr.zmat ├── c4c4im.zmat ├── c4fc1fsi.zmat ├── c4pyri.zmat ├── c6c1im.zmat ├── c8c1im.zmat ├── c8fc1im.zmat ├── c8isoqui.xyz ├── chexoat.xyz ├── cholinium.xyz ├── dca.zmat ├── des.ff ├── fsi.zmat ├── gua.zmat ├── il.ff ├── ilff_structures.pdf ├── isoval.xyz ├── ntf2.zmat ├── oac.zmat ├── old.il.ff ├── otf.zmat ├── phoac.zmat ├── pmbzoat.xyz ├── tfa.zmat ├── topologies ├── README.md ├── bpybf4 │ ├── bf4.itp │ ├── bpy.itp │ ├── ff.itp │ └── topol.top ├── bpycl │ ├── bpy.itp │ ├── chloride.itp │ ├── ff.itp │ └── topol.top ├── bpydca │ ├── bpy.itp │ ├── dca.itp │ ├── ff.itp │ └── topol.top ├── bpypf6 │ ├── bpy.itp │ ├── ff.itp │ ├── pf6.itp │ └── topol.top ├── bpytf │ ├── bpy.itp │ ├── ff.itp │ ├── tf.itp │ └── topol.top ├── bpytfsi │ ├── bpy.itp │ ├── ff.itp │ ├── tfsi.itp │ └── topol.top ├── py14bf4 │ ├── bf4.gro │ ├── bf4.itp │ ├── ff.itp │ ├── pyr.gro │ ├── pyr.itp │ └── topol.top ├── py14cl │ ├── chloride.itp │ ├── cl.gro │ ├── ff.itp │ ├── pyr.gro │ ├── pyr.itp │ └── topol.top ├── py14dca │ ├── dca.gro │ ├── dca.itp │ ├── ff.itp │ ├── pyr.gro │ ├── pyr.itp │ └── topol.top ├── py14fsi │ ├── ff.itp │ ├── fsi.gro │ ├── fsi.itp │ ├── pyr.gro │ ├── pyr.itp │ └── topol.top ├── py14tf │ ├── Tf.gro │ ├── ff.itp │ ├── pyr.gro │ ├── pyr.itp │ ├── tf.itp │ └── topol.top └── py14tfsi │ ├── ff.itp │ ├── pyr.gro │ ├── pyr.itp │ ├── tfsi.gro │ ├── tfsi.itp │ └── topol.top └── tso.zmat /.gitignore: -------------------------------------------------------------------------------- 1 | examples/*.ff 2 | examples/*.xyz 3 | examples/*.inp 4 | examples/*.lmp 5 | examples/FIELD 6 | examples/CONFIG 7 | -------------------------------------------------------------------------------- /BF4.zmat: -------------------------------------------------------------------------------- 1 | BF4- 2 | 3 | 1 B 4 | 2 FB 1 1.394 5 | 3 FB 1 1.394 2 109.5 6 | 4 FB 1 1.394 2 109.5 3 120.0 7 | 5 FB 1 1.394 2 109.5 3 -120.0 8 | 9 | il.ff 10 | -------------------------------------------------------------------------------- /Br.zmat: -------------------------------------------------------------------------------- 1 | Br- 2 | 3 | 1 Br 4 | 5 | il.ff 6 | -------------------------------------------------------------------------------- /CCN3.xyz: -------------------------------------------------------------------------------- 1 | 7 2 | C(CN)3- il.ff 3 | C3A -0.33829 -0.05384 -0.10704 4 | CN 1.06483 -0.12753 -0.26141 5 | CN -0.90375 0.90027 0.76928 6 | CN -1.17580 -0.93634 -0.82662 7 | NC 2.21625 -0.18820 -0.38787 8 | NC -1.36776 1.68302 1.48861 9 | NC -1.86303 -1.66070 -1.41688 10 | -------------------------------------------------------------------------------- /Cl.zmat: -------------------------------------------------------------------------------- 1 | Cl- 2 | 3 | 1 Cl 4 | 5 | il.ff 6 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2019 Agilio Padua 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /N1110.zmat: -------------------------------------------------------------------------------- 1 | N1110+ 2 | 3 | 1 N3 4 | 2 C1 1 1.471 5 | 3 C1 1 1.471 2 109.5 6 | 4 C1 1 1.471 2 109.5 3 120.0 7 | 5 H3 1 1.090 2 109.5 3 240.0 8 | 6 H1 2 1.090 1 109.5 3 60.0 9 | 7 H1 2 1.090 1 109.5 3 180.0 10 | 8 H1 2 1.090 1 109.5 3 300.0 11 | 9 H1 3 1.090 1 109.5 4 60.0 12 | 10 H1 3 1.090 1 109.5 4 180.0 13 | 11 H1 3 1.090 1 109.5 4 300.0 14 | 12 H1 4 1.090 1 109.5 5 60.0 15 | 13 H1 4 1.090 1 109.5 5 180.0 16 | 14 H1 4 1.090 1 109.5 5 300.0 17 | 18 | il.ff 19 | -------------------------------------------------------------------------------- /N1111.zmat: -------------------------------------------------------------------------------- 1 | N1111+ 2 | 3 | 1 N4 4 | 2 C1 1 1.471 5 | 3 C1 1 1.471 2 109.5 6 | 4 C1 1 1.471 2 109.5 3 120.0 7 | 5 C1 1 1.471 2 109.5 3 240.0 8 | 6 H1 2 1.090 1 109.5 3 60.0 9 | 7 H1 2 1.090 1 109.5 3 180.0 10 | 8 H1 2 1.090 1 109.5 3 300.0 11 | 9 H1 3 1.090 1 109.5 4 60.0 12 | 10 H1 3 1.090 1 109.5 4 180.0 13 | 11 H1 3 1.090 1 109.5 4 300.0 14 | 12 H1 4 1.090 1 109.5 5 60.0 15 | 13 H1 4 1.090 1 109.5 5 180.0 16 | 14 H1 4 1.090 1 109.5 5 300.0 17 | 15 H1 5 1.090 1 109.5 2 60.0 18 | 16 H1 5 1.090 1 109.5 2 180.0 19 | 17 H1 5 1.090 1 109.5 2 300.0 20 | 21 | il.ff 22 | -------------------------------------------------------------------------------- /N2220.xyz: -------------------------------------------------------------------------------- 1 | 23 2 | triethylammonium il.ff 3 | N3 0.00000 0.00000 0.00000 4 | C1A 1.35415 -0.41156 -0.47087 5 | C1A -1.03339 -0.96717 -0.47074 6 | C1A -0.32073 1.37841 -0.47079 7 | CE 1.82045 -1.77684 0.05640 8 | H1 2.11747 0.29570 -0.09133 9 | H1 1.40122 -0.41216 -1.58306 10 | HC 1.22172 -2.61522 -0.34939 11 | HC 1.78877 -1.79290 1.16636 12 | HC 2.86804 -1.95240 -0.26845 13 | H1 -1.31481 1.68586 -0.09099 14 | H1 -0.34395 1.41958 -1.58297 15 | CE 0.62852 2.46492 0.05649 16 | HC 1.65385 2.36580 -0.34955 17 | HC 0.65852 2.44528 1.16644 18 | HC 0.25659 3.45996 -0.26807 19 | H1 -0.80289 -1.98154 -0.09014 20 | H1 -1.05679 -1.00854 -1.58290 21 | CE -2.44923 -0.68768 0.05535 22 | HC -2.44803 -0.65089 1.16526 23 | HC -3.12491 -1.50748 -0.26900 24 | HC -2.87562 0.24953 -0.35190 25 | H3 0.00000 0.00000 1.04814 26 | -------------------------------------------------------------------------------- /N2222.xyz: -------------------------------------------------------------------------------- 1 | 29 2 | N2222+ il.ff 3 | N4 -1.56714 -1.12928 0.83374 4 | C1A -0.17714 -0.54716 0.83557 5 | C1A -1.52602 -2.63357 0.75365 6 | C1A -2.34880 -0.66545 -0.36828 7 | C1A -2.21662 -0.67095 2.11401 8 | H1 0.37265 -0.87300 1.74466 9 | H1 -0.22613 0.55902 0.92988 10 | H1 -1.87505 -1.04135 -1.30060 11 | H1 -3.35831 -1.12996 -0.37042 12 | H1 -1.07448 -2.95295 -0.21020 13 | H1 -2.55859 -3.04284 0.71849 14 | H1 -2.20849 0.43882 2.17091 15 | H1 -1.60880 -0.99199 2.98719 16 | CE 0.70738 -0.87570 -0.39215 17 | CE -0.76992 -3.36218 1.89166 18 | CE -2.53457 0.86439 -0.51904 19 | CE -3.67138 -1.14368 2.35446 20 | HC -4.28352 -0.84853 1.52798 21 | HC -4.04677 -0.69981 3.25277 22 | HC -3.68912 -2.20937 2.44879 23 | HC -3.10136 1.06944 -1.40312 24 | HC -1.57621 1.33450 -0.59275 25 | HC -3.05451 1.24638 0.33457 26 | HC -0.80912 -4.41864 1.72659 27 | HC -1.22877 -3.13055 2.83012 28 | HC 0.25060 -3.04084 1.90466 29 | HC 0.20349 -0.57265 -1.28611 30 | HC 0.89258 -1.92898 -0.42670 31 | HC 1.63730 -0.35250 -0.31203 32 | -------------------------------------------------------------------------------- /N4444.xyz: -------------------------------------------------------------------------------- 1 | 53 2 | N4444+ il.ff 3 | N4 -1.56714 -1.12928 0.83374 4 | C1A -0.17714 -0.54716 0.83557 5 | C1A -1.52602 -2.63357 0.75365 6 | C1A -2.34880 -0.66545 -0.36828 7 | C1A -2.21662 -0.67095 2.11401 8 | H1 0.37265 -0.87300 1.74466 9 | H1 -0.22613 0.55902 0.92988 10 | H1 -1.87505 -1.04135 -1.30060 11 | H1 -3.35831 -1.12996 -0.37042 12 | H1 -1.07448 -2.95295 -0.21020 13 | H1 -2.55859 -3.04284 0.71849 14 | H1 -2.20849 0.43882 2.17091 15 | H1 -1.60880 -0.99199 2.98719 16 | C2 0.70738 -0.87570 -0.39215 17 | C2 -0.76992 -3.36218 1.89166 18 | C2 -2.53457 0.86439 -0.51904 19 | C2 -3.67138 -1.14368 2.35446 20 | HC 0.24060 -0.49197 -1.32187 21 | HC 0.85912 -1.97052 -0.48071 22 | HC 0.29404 -3.05070 1.91372 23 | HC -1.23841 -3.14325 2.87253 24 | HC -1.55117 1.36881 -0.60851 25 | HC -3.08278 1.27754 0.35175 26 | HC -3.71944 -2.25080 2.39279 27 | HC -4.33886 -0.77347 1.55014 28 | CS 2.08736 -0.21931 -0.25341 29 | CS -0.81095 -4.88133 1.67970 30 | CS -3.34503 1.18715 -1.78133 31 | CS -4.19983 -0.60369 3.68996 32 | CT 2.97286 -0.53279 -1.45639 33 | CT -0.07002 -5.61584 2.79374 34 | CT -3.53733 2.69232 -1.94582 35 | CT -5.63382 -1.06092 3.94336 36 | HC 2.58868 -0.59264 0.66624 37 | HC 1.97088 0.88365 -0.17336 38 | HC 3.12594 -1.62925 -1.54810 39 | HC 3.96218 -0.04540 -1.32744 40 | HC 2.50683 -0.14989 -2.38928 41 | HC -1.86717 -5.22865 1.66380 42 | HC -0.33697 -5.13646 0.70671 43 | HC -0.53720 -5.39741 3.77767 44 | HC -0.11700 -6.71044 2.61325 45 | HC 0.99621 -5.30505 2.81875 46 | HC -5.68458 -2.17000 3.98143 47 | HC -5.98765 -0.65547 4.91462 48 | HC -6.30480 -0.69211 3.13848 49 | HC -3.55691 -0.96698 4.52132 50 | HC -4.17572 0.50797 3.68010 51 | HC -4.12582 2.89407 -2.86556 52 | HC -2.55325 3.19999 -2.03493 53 | HC -4.08567 3.10921 -1.07428 54 | HC -4.34456 0.70402 -1.71813 55 | HC -2.81526 0.79477 -2.67680 56 | -------------------------------------------------------------------------------- /Na.zmat: -------------------------------------------------------------------------------- 1 | Na+ 2 | 3 | 1 Na 4 | 5 | il.ff 6 | -------------------------------------------------------------------------------- /P1111.zmat: -------------------------------------------------------------------------------- 1 | P1111+ 2 | 3 | 1 P3 4 | 2 C1P 1 1.8104 5 | 3 C1P 1 1.8104 2 109.5 6 | 4 H1 3 1.0837 1 109.5 2 300.0 7 | 5 H1 3 1.0837 1 109.5 2 180.0 8 | 6 H1 3 1.0837 1 109.5 2 60.0 9 | 7 H1 2 1.0837 1 109.5 3 180.0 10 | 8 H1 2 1.0837 1 109.5 3 60.0 11 | 9 H1 2 1.0837 1 109.5 3 300.0 12 | 10 C1P 1 1.8104 2 109.5 3 240.0 13 | 11 H1 10 1.0837 1 109.5 2 300.0 14 | 12 H1 10 1.0837 1 109.5 2 180.0 15 | 13 H1 10 1.0837 1 109.5 2 60.0 16 | 14 C1P 1 1.8104 2 109.5 3 120.0 17 | 15 H1 14 1.0837 1 109.5 2 300.0 18 | 16 H1 14 1.0837 1 109.5 2 180.0 19 | 17 H1 14 1.0837 1 109.5 2 60.0 20 | 21 | il.ff 22 | -------------------------------------------------------------------------------- /P1112O2.xyz: -------------------------------------------------------------------------------- 1 | 27 2 | P1112O2 il.ff 3 | P3 -0.01722 -0.43974 0.73834 4 | C1P 1.41251 0.21160 1.67426 5 | C1P -1.50726 0.29181 1.50722 6 | C1PS 0.09440 -0.04273 -1.04073 7 | C1P -0.07132 -2.23935 0.91900 8 | CSO 0.56898 1.38157 -1.29434 9 | OY -0.16680 2.23466 -0.43344 10 | CSO 0.13304 3.62672 -0.60473 11 | CT -0.68482 4.42088 0.39155 12 | H1 -0.90079 -0.22105 -1.45134 13 | H1 0.79157 -0.75752 -1.47732 14 | H1 0.81568 -2.67623 0.46015 15 | H1 -0.97494 -2.60128 0.43032 16 | H1 -0.10630 -2.50408 1.97726 17 | HY 1.64408 1.46242 -1.09375 18 | HY 0.39863 1.64436 -2.34557 19 | HY 1.20875 3.78535 -0.45121 20 | HY -0.10628 3.91925 -1.63449 21 | HC -1.75304 4.25619 0.23489 22 | HC -0.43234 4.14115 1.41735 23 | HC -0.48468 5.48797 0.27412 24 | H1 -2.38016 -0.05708 0.99613 25 | H1 -1.45657 1.35844 1.43922 26 | H1 -1.55658 0.00195 2.53603 27 | H1 2.31771 -0.18600 1.26507 28 | H1 1.32817 -0.07730 2.70106 29 | H1 1.42819 1.27919 1.60425 30 | -------------------------------------------------------------------------------- /P111i4.xyz: -------------------------------------------------------------------------------- 1 | 26 2 | p111i4+ il.ff 3 | P3 -1.80917 2.07160 0.01629 4 | C1P -1.50312 3.58599 -0.93518 5 | H1 -2.43154 3.93120 -1.39476 6 | H1 -0.77597 3.39560 -1.72723 7 | H1 -1.12458 4.37422 -0.28122 8 | C1P -3.17668 2.37782 1.16941 9 | H1 -3.90953 3.04866 0.71625 10 | H1 -2.80086 2.83739 2.08597 11 | H1 -3.67178 1.43884 1.42557 12 | C1P -2.29606 0.74441 -1.12182 13 | H1 -1.46401 0.48266 -1.77846 14 | H1 -3.13902 1.06742 -1.73626 15 | H1 -2.59194 -0.14361 -0.55925 16 | CPI4 -0.34853 1.54623 0.97315 17 | CI4 0.97605 1.44450 0.16909 18 | H1 -0.59596 0.56448 1.38402 19 | H1 -0.21819 2.21341 1.82854 20 | CT 1.73586 2.79065 0.14074 21 | HC 1.14811 3.57382 -0.33598 22 | HC 2.66799 2.69056 -0.42065 23 | HC 1.98281 3.11937 1.15319 24 | CT 1.89023 0.36164 0.78322 25 | HC 0.75098 1.14502 -0.85720 26 | HI4 2.13641 0.60198 1.82048 27 | HC 2.82242 0.28001 0.21869 28 | HC 1.39995 -0.61438 0.76238 29 | -------------------------------------------------------------------------------- /P4444.xyz: -------------------------------------------------------------------------------- 1 | 53 2 | P4444+ il.ff 3 | P3 -1.55069 -1.10117 0.80137 4 | C1P 0.13685 -0.41966 0.76957 5 | C1P -1.49426 -2.91898 0.73190 6 | C1P -2.49099 -0.50275 -0.63766 7 | C1P -2.35505 -0.56446 2.34333 8 | H1 0.63438 -0.68731 1.70452 9 | H1 0.07083 0.67018 0.74250 10 | H1 -1.95015 -0.77931 -1.54538 11 | H1 -3.44992 -1.02541 -0.66443 12 | H1 -1.04477 -3.21595 -0.21833 13 | H1 -2.51832 -3.29894 0.73262 14 | H1 -2.34064 0.52709 2.38027 15 | H1 -1.76034 -0.91990 3.18769 16 | C2 0.97997 -0.91635 -0.42280 17 | C2 -0.70757 -3.55174 1.89770 18 | C2 -2.73496 1.02020 -0.62493 19 | C2 -3.80565 -1.06888 2.48428 20 | HC 0.48420 -0.65086 -1.35935 21 | HC 1.06072 -2.00507 -0.38693 22 | HC 0.31511 -3.16743 1.90203 23 | HC -1.17081 -3.27216 2.84679 24 | HC -1.77747 1.54554 -0.59714 25 | HC -3.29070 1.29534 0.27435 26 | HC -3.81688 -2.16115 2.46931 27 | HC -4.39996 -0.71948 1.63682 28 | CT2 2.39470 -0.30131 -0.39895 29 | CT2 -0.67520 -5.08934 1.77772 30 | CT2 -3.52952 1.46741 -1.86940 31 | CT2 -4.44371 -0.56876 3.79678 32 | CT 3.24770 -0.81506 -1.57335 33 | CT 0.10994 -5.72444 2.93985 34 | CT -3.79737 2.98343 -1.84704 35 | CT -5.89233 -1.07008 3.94058 36 | HC 2.89063 -0.55333 0.54171 37 | HC 2.32437 0.78785 -0.45382 38 | HC 3.35751 -1.90095 -1.52399 39 | HC 4.24379 -0.36804 -1.54062 40 | HC 2.78586 -0.55504 -2.52864 41 | HC -1.69557 -5.48077 1.77636 42 | HC -0.21036 -5.37561 0.83095 43 | HC -0.35099 -5.47512 3.89850 44 | HC 0.12239 -6.81182 2.83762 45 | HC 1.14290 -5.36865 2.94737 46 | HC -5.92338 -2.16210 3.95048 47 | HC -6.32706 -0.70600 4.87414 48 | HC -6.50843 -0.71186 3.11252 49 | HC -3.85575 -0.91793 4.64920 50 | HC -4.43778 0.52388 3.81671 51 | HC -4.35873 3.28105 -2.73548 52 | HC -2.85810 3.54120 -1.83152 53 | HC -4.38030 3.25896 -0.96499 54 | HC -4.48329 0.93524 -1.90892 55 | HC -2.97176 1.21315 -2.77415 56 | -------------------------------------------------------------------------------- /P66614.zmat: -------------------------------------------------------------------------------- 1 | P66614+ 2 | 3 | 1 P3 4 | 2 C1P 1 1.81 5 | 3 C1P 1 1.81 2 109.5 6 | 4 C1P 1 1.81 2 109.5 3 120.0 7 | 5 C1P 1 1.81 2 109.5 3 240.0 8 | 6 C2 2 1.53 1 115.2 3 60.0 9 | 7 H1 2 1.09 1 110.1 3 180.0 10 | 8 H1 2 1.09 1 110.1 3 300.0 11 | 9 H1 3 1.09 1 110.1 4 60.0 12 | 10 H1 3 1.09 1 110.1 4 180.0 13 | 11 C2 3 1.53 1 115.2 4 300.0 14 | 12 C2 4 1.53 1 115.2 5 60.0 15 | 13 H1 4 1.09 1 110.1 5 180.0 16 | 14 H1 4 1.09 1 110.1 5 300.0 17 | 15 H1 5 1.09 1 110.1 2 60.0 18 | 16 H1 5 1.09 1 110.1 2 180.0 19 | 17 C2 5 1.53 1 115.2 2 300.0 20 | 18 CS 6 1.53 2 112.7 1 180.0 21 | 19 HC 6 1.09 2 110.7 1 60.0 22 | 20 HC 6 1.09 2 110.7 1 300.0 23 | 21 CS 18 1.53 6 112.7 2 180.0 24 | 22 HC 18 1.09 6 110.7 2 60.0 25 | 23 HC 18 1.09 6 110.7 2 300.0 26 | 24 CS 21 1.53 18 112.7 6 180.0 27 | 25 HC 21 1.09 18 110.7 6 60.0 28 | 26 HC 21 1.09 18 110.7 6 300.0 29 | 27 CT 24 1.53 21 112.7 18 180.0 30 | 28 HC 24 1.09 21 110.7 18 60.0 31 | 29 HC 24 1.09 21 110.7 18 300.0 32 | 30 HC 27 1.09 24 110.7 21 180.0 33 | 31 HC 27 1.09 24 110.7 21 60.0 34 | 32 HC 27 1.09 24 110.7 21 300.0 35 | 33 CS 11 1.53 3 112.7 1 180.0 36 | 34 HC 11 1.09 3 110.7 1 60.0 37 | 35 HC 11 1.09 3 110.7 1 300.0 38 | 36 CS 33 1.53 11 112.7 3 180.0 39 | 37 HC 33 1.09 11 110.7 3 60.0 40 | 38 HC 33 1.09 11 110.7 3 300.0 41 | 39 CS 36 1.53 33 112.7 11 180.0 42 | 40 HC 36 1.09 33 110.7 11 60.0 43 | 41 HC 36 1.09 33 110.7 11 300.0 44 | 42 CT 39 1.53 36 112.7 33 180.0 45 | 43 HC 39 1.09 36 110.7 33 60.0 46 | 44 HC 39 1.09 36 110.7 33 300.0 47 | 45 HC 42 1.09 39 110.7 36 180.0 48 | 46 HC 42 1.09 39 110.7 36 60.0 49 | 47 HC 42 1.09 39 110.7 36 300.0 50 | 48 CS 12 1.53 4 112.7 1 180.0 51 | 49 HC 12 1.09 4 110.7 1 60.0 52 | 50 HC 12 1.09 4 110.7 1 300.0 53 | 51 CS 48 1.53 12 112.7 4 180.0 54 | 52 HC 48 1.09 12 110.7 4 60.0 55 | 53 HC 48 1.09 12 110.7 4 300.0 56 | 54 CS 51 1.53 48 112.7 12 180.0 57 | 55 HC 51 1.09 48 110.7 12 60.0 58 | 56 HC 51 1.09 48 110.7 12 300.0 59 | 57 CT 54 1.53 51 112.7 48 180.0 60 | 58 HC 54 1.09 51 110.7 48 60.0 61 | 59 HC 54 1.09 51 110.7 48 300.0 62 | 60 HC 57 1.09 54 110.7 51 180.0 63 | 61 HC 57 1.09 54 110.7 51 60.0 64 | 62 HC 57 1.09 54 110.7 51 300.0 65 | 63 CS 17 1.53 5 112.7 1 180.0 66 | 64 HC 17 1.09 5 110.7 1 60.0 67 | 65 HC 17 1.09 5 110.7 1 300.0 68 | 66 CS 63 1.53 17 112.7 5 180.0 69 | 67 HC 63 1.09 17 110.7 5 60.0 70 | 68 HC 63 1.09 17 110.7 5 300.0 71 | 69 CS 66 1.53 63 112.7 17 180.0 72 | 70 HC 66 1.09 63 110.7 17 60.0 73 | 71 HC 66 1.09 63 110.7 17 300.0 74 | 72 CS 69 1.53 66 112.7 63 180.0 75 | 73 HC 69 1.09 66 110.7 63 60.0 76 | 74 HC 69 1.09 66 110.7 63 300.0 77 | 75 CS 72 1.53 69 110.7 66 180.0 78 | 76 HC 72 1.09 69 110.7 66 60.0 79 | 77 HC 72 1.09 69 110.7 66 300.0 80 | 78 CS 75 1.53 72 112.7 69 180.0 81 | 79 HC 75 1.09 72 110.7 69 60.0 82 | 80 HC 75 1.09 72 110.7 69 300.0 83 | 81 CS 78 1.53 75 112.7 72 180.0 84 | 82 HC 78 1.09 75 110.7 72 60.0 85 | 83 HC 78 1.09 75 110.7 72 300.0 86 | 84 CS 81 1.53 78 112.7 75 180.0 87 | 85 HC 81 1.09 78 110.7 75 60.0 88 | 86 HC 81 1.09 78 110.7 75 300.0 89 | 87 CS 84 1.53 81 110.7 78 180.0 90 | 88 HC 84 1.09 81 110.7 78 60.0 91 | 89 HC 84 1.09 81 110.7 78 300.0 92 | 90 CS 87 1.53 84 112.7 81 180.0 93 | 91 HC 87 1.09 84 110.7 81 60.0 94 | 92 HC 87 1.09 84 110.7 81 300.0 95 | 93 CS 90 1.53 87 112.7 84 180.0 96 | 94 HC 90 1.09 87 110.7 84 60.0 97 | 95 HC 90 1.09 87 110.7 84 300.0 98 | 96 CT 93 1.53 90 112.7 87 180.0 99 | 97 HC 93 1.09 90 110.7 87 60.0 100 | 98 HC 93 1.09 90 110.7 87 300.0 101 | 99 HC 96 1.09 93 110.7 90 180.0 102 | 100 HC 96 1.09 93 110.7 90 60.0 103 | 101 HC 96 1.09 93 110.7 90 300.0 104 | 105 | il.ff 106 | -------------------------------------------------------------------------------- /PF6.zmat: -------------------------------------------------------------------------------- 1 | PF6- 2 | 3 | 1 P 4 | 2 FP 1 1.606 5 | 3 FP 1 1.606 2 90.0 6 | 4 FP 1 1.606 2 90.0 3 90.0 7 | 5 FP 1 1.606 2 90.0 3 -90.0 8 | 6 FP 1 1.606 2 90.0 3 180.0 9 | 7 FP 1 1.606 2 180.0 3 0.0 10 | 11 | il.ff 12 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | CL&P force field for ionic liquids 2 | ============================= 3 | 4 | [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.593705.svg)](http://dx.doi.org/10.5281/zenodo.593705) 5 | 6 | _[Agilio Padua](http://perso.ens-lyon.fr/agilio.padua)_ 7 | 8 | _series of papers by A. Padua, J.N. Canongia Lopes et al. J Phys Chem 9 | B (since 2004)_ 10 | 11 | Contents 12 | -------- 13 | 14 | * `il.ff`: database of force field parameters for ions of several 15 | ionic liquids (under construction, compatible with the 16 | [fftool](http://www.github.com/agiliopadua/fftool) script to 17 | create input files for molecular simulation using the 18 | [LAMMPS](http://lammps.sandia.gov), 19 | [DL_POLY](http://www.stfc.ac.uk/CSE/randd/ccg/software/DL_POLY/25526.aspx) 20 | or [GROMACS](http://www.gromacs.org) 21 | molecular dynamics codes. 22 | 23 | * `old.il.ff`: database of force field parameters for ions of several ionic 24 | liquids (previous format, complete with many ions). 25 | 26 | * `*.zmat, *.mol, *.xyz`: input files for ions. 27 | 28 | * `topologies`: topology files in gromacs format for pyridinium and 29 | pyrrolidinium ionic liquids, with refined parameters for better 30 | representation of transport properties. Contributed by Vitaly 31 | Chaban. 32 | 33 | 34 | Requirements 35 | ------------ 36 | 37 | * [fftool](http://www.github.com/agiliopadua/fftool) 38 | 39 | * [Python](http://www.python.org/) 40 | 41 | * [Packmol](http://www.ime.unicamp.br/~martinez/packmol/) 42 | 43 | 44 | Obtaining 45 | --------- 46 | 47 | Download the files or else clone the repository (easier to stay updated): 48 | 49 | git clone https://github.com/agiliopadua/ilff.git 50 | 51 | 52 | How to use 53 | ---------- 54 | 55 | How to build an initial configuration of a molecular or ionic system. 56 | 57 | 1. For each molecule, ion or fragment of a material prepare a file 58 | with atomic coordinates and/or connectivity (covalent bonds). The 59 | formats accepted by this tool are `.zmat`, `.mol` or 60 | `.xyz`. Detailed information is available in the 61 | [fftool](http://www.github.com/agiliopadua/fftool) page. 62 | 63 | 64 | 2. Use the `fftool` script to create `.xyz` files for the molecules 65 | in your system and an input file for 66 | [Packmol](http://www.ime.unicamp.br/~martinez/packmol/). For help 67 | type `fftool -h`. For example, to build a simulation box with 20 68 | ion pairs and a density of 3.0 mol/L do: 69 | 70 | fftool 20 c4c1im.zmat 20 ntf2.zmat --rho 3.0 71 | 72 | 3. Use Packmol with the `pack.inp` file just created to buid the 73 | simulation box (adjust the density if necessary): 74 | 75 | packmol < pack.inp 76 | 77 | Atom coordinates will be written to a file `simbox.xyz`. You can 78 | use a molecular viewer such as VMD to look at the `.xyz` files. 79 | 80 | 4. Use `fftool` to build the input files for LAMMPS, DL_POLY or Gromacs 81 | containing the force field and the coordinates: 82 | 83 | fftool 20 c4c1im.zmat 20 ntf2.zmat --lammps 84 | 85 | Information on the force field file format and on more geeral or 86 | advanced used is available at the 87 | [fftool](http://www.github.com/agiliopadua/fftool) page. 88 | 89 | 90 | References 91 | ---------- 92 | 93 | * [Packmol](http://www.ime.unicamp.br/~martinez/packmol/): 94 | L. Martinez et al. J Comp Chem 30 (2009) 2157, DOI: 95 | [10.1002/jcc.21224](http://dx.doi.org/10.1002/jcc.21224) 96 | 97 | * [LAMMPS](http://lammps.sandia.gov/): S. Plimton, J Comp Phys 98 | 117 (1995) 1, DOI: 99 | [10.1006/jcph.1995.1039](http://dx.doi.org/10.1006/jcph.1995.1039) 100 | 101 | * [DL_POLY](http://www.stfc.ac.uk/CSE/randd/ccg/software/DL_POLY/25526.aspx): 102 | I.T. Todorov and W. Smith, Daresbury Lab. 103 | 104 | * [GROMACS](http://www.gromacs.org) M. Abraham , D. van der Spoel, 105 | B. Hess, E. Lindahl, et al. 106 | 107 | * IL force field: J.N. Canongia Lopes, A.A.H. Padua et al. 108 | J Phys Chem B 108 (2004) 2038, DOI: 109 | [10.1021/jp0362133](http://dx.doi.org/10.1021/jp0362133); 110 | J Phys Chem B 108 (2004) 11250, DOI: 111 | [10.1021/jp0476996](http://dx.doi.org/10.1021/jp0476996); 112 | J Phys Chem B 108 (2004) 16893, DOI: 113 | [10.1021/jp0476545](http://dx.doi.org/10.1021/jp0476545); 114 | J Phys Chem B 110 (2006) 19586, DOI: 115 | [10.1021/jp063901o](http://dx.doi.org/10.1021/jp063901o); 116 | J Phys Chem B 110 (2008) 5039, DOI: 117 | [10.1021/jp800281e](http://dx.doi.org/10.1021/jp800281e); 118 | J Phys Chem B 110 (2010) 3592, DOI: 119 | [10.1021/jp9120468](http://dx.doi.org/10.1021/jp9120468) 120 | 121 | * OPLS-AA force field: W.L. Jorgensen et al. JACS 118 (1996) 11225, 122 | DOI: [10.1021/ja9621760](http://dx.doi.org/10.1021/ja9621760) 123 | 124 | * AMBER force field: P. Kollman et al. JACS 117 (1995) 5179, DOI: 125 | [10.1021/ja00124a002](http://dx.doi.org/10.1021/ja00124a002) 126 | -------------------------------------------------------------------------------- /SCN.zmat: -------------------------------------------------------------------------------- 1 | thiocyanate 2 | 3 | SK 4 | CK 1 1.66 5 | NK 2 1.19 1 180.0 6 | 7 | il.ff 8 | -------------------------------------------------------------------------------- /benzc1im.zmat: -------------------------------------------------------------------------------- 1 | benzc1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.08 1 125.1 3 180.0 10 | 8 C1T 3 1.529 2 120.0 1 180.0 11 | 9 HCW 4 1.08 3 126.5 2 180.0 12 | 10 HCW 5 1.08 4 126.5 3 180.0 13 | 11 H1 6 1.09 1 109.5 5 60.0 14 | 12 H1 6 1.09 1 109.5 5 180.0 15 | 13 H1 6 1.09 1 109.5 5 300.0 16 | 14 H1 8 1.09 3 109.5 2 30.0 17 | 15 H1 8 1.09 3 109.5 2 150.0 18 | 16 CAT 8 1.51 3 109.5 2 270.0 19 | 17 CAO 16 1.40 8 120.0 3 180.0 20 | 18 CAM 17 1.40 16 120.0 8 180.0 21 | 19 CAP 18 1.40 17 120.0 16 0.0 22 | 20 CAM 19 1.40 18 120.0 17 0.0 23 | 21 CAO 20 1.40 19 120.0 18 0.0 24 | 22 HAT 17 1.08 16 120.0 8 0.0 25 | 23 HAT 18 1.08 17 120.0 16 180.0 26 | 24 HAT 19 1.08 18 120.0 17 180.0 27 | 25 HAT 20 1.08 19 120.0 18 180.0 28 | 26 HAT 21 1.08 20 120.0 19 180.0 29 | 30 | connect 5 1 31 | connect 21 16 32 | 33 | il.ff 34 | -------------------------------------------------------------------------------- /beti.zmat: -------------------------------------------------------------------------------- 1 | beti- 2 | 3 | 1 C1F 4 | 2 CEF 1 1.529 5 | 3 F1 1 1.332 2 107.1 6 | 4 F1 1 1.332 2 107.1 3 120.0 7 | 5 SBT 1 1.818 2 111.8 3 -120.0 8 | 6 NBT 5 1.700 1 102.6 3 60.0 9 | 7 OBT 5 1.443 1 102.6 6 120.0 10 | 8 OBT 5 1.443 1 102.6 6 -120.0 11 | 9 SBT 6 1.700 5 120.0 1 90.0 12 | 10 OBT 9 1.443 6 102.6 5 -30.0 13 | 11 OBT 9 1.443 6 102.6 5 -150.0 14 | 12 C1F 9 1.818 6 102.6 5 90.0 15 | 13 CEF 12 1.529 9 111.8 6 180.0 16 | 14 F1 12 1.332 9 107.1 13 120.0 17 | 15 F1 12 1.332 9 107.1 13 240.0 18 | 16 F 13 1.332 12 107.1 9 60.0 19 | 17 F 13 1.332 12 107.1 9 -60.0 20 | 18 F 13 1.332 12 107.1 9 180.0 21 | 19 F 2 1.332 1 109.5 5 60.0 22 | 20 F 2 1.332 1 109.5 5 -60.0 23 | 21 F 2 1.332 1 109.5 5 180.0 24 | 25 | il.ff 26 | -------------------------------------------------------------------------------- /c12c1im.zmat: -------------------------------------------------------------------------------- 1 | c12c1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 C2 8 1.529 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 CS 14 1.529 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 CS 17 1.529 14 109.5 8 180.0 23 | 21 HC 17 1.090 14 109.5 8 60.0 24 | 22 HC 17 1.090 14 109.5 8 300.0 25 | 23 CS 20 1.529 17 109.5 14 180.0 26 | 24 HC 20 1.090 17 109.5 14 60.0 27 | 25 HC 20 1.090 17 109.5 14 300.0 28 | 26 CS 23 1.529 20 109.5 17 180.0 29 | 27 HC 23 1.090 20 109.5 17 60.0 30 | 28 HC 23 1.090 20 109.5 17 300.0 31 | 29 CS 26 1.529 23 109.5 20 180.0 32 | 30 HC 26 1.090 23 109.5 20 60.0 33 | 31 HC 26 1.090 23 109.5 20 300.0 34 | 32 CS 29 1.529 26 109.5 23 180.0 35 | 33 HC 29 1.090 26 109.5 23 60.0 36 | 34 HC 29 1.090 26 109.5 23 300.0 37 | 35 CS 32 1.529 29 109.5 26 180.0 38 | 36 HC 32 1.090 29 109.5 26 60.0 39 | 37 HC 32 1.090 29 109.5 26 300.0 40 | 38 CS 35 1.529 32 109.5 29 180.0 41 | 39 HC 35 1.090 32 109.5 29 60.0 42 | 40 HC 35 1.090 32 109.5 29 300.0 43 | 41 CS 38 1.529 35 109.5 32 180.0 44 | 42 HC 38 1.090 35 109.5 32 60.0 45 | 43 HC 38 1.090 35 109.5 32 300.0 46 | 44 CT 41 1.529 38 109.5 35 180.0 47 | 45 HC 41 1.090 38 109.5 35 60.0 48 | 46 HC 41 1.090 38 109.5 35 300.0 49 | 47 HC 44 1.090 41 109.5 38 180.0 50 | 48 HC 44 1.090 41 109.5 38 60.0 51 | 49 HC 44 1.090 41 109.5 38 300.0 52 | 53 | connect 5 1 54 | 55 | improper 5 2 1 6 56 | improper 1 3 2 7 57 | improper 2 4 3 8 58 | improper 3 5 4 9 59 | improper 4 1 5 10 60 | 61 | il.ff 62 | -------------------------------------------------------------------------------- /c1SO3.zmat: -------------------------------------------------------------------------------- 1 | methylsulfonate 2 | 3 | 1 SO 4 | 2 OS3 1 1.455 5 | 3 OS3 1 1.455 2 109.5 6 | 4 OS3 1 1.455 2 109.5 3 120.0 7 | 5 CS3 1 1.792 2 109.5 3 240.0 8 | 6 HS3 5 1.090 1 109.5 2 60.0 9 | 7 HS3 5 1.090 1 109.5 2 180.0 10 | 8 HS3 5 1.090 1 109.5 2 300.0 11 | 12 | il.ff 13 | -------------------------------------------------------------------------------- /c1SO4.zmat: -------------------------------------------------------------------------------- 1 | methylsulfate 2 | 3 | 1 HS4 4 | 2 CS4 1 1.090 5 | 3 OC4 2 1.529 1 109.5 6 | 4 HS4 2 1.090 1 109.5 3 120.0 7 | 5 HS4 2 1.090 1 109.5 3 240.0 8 | 6 SO 3 1.810 2 109.5 1 180.0 9 | 7 OS4 6 1.810 3 109.5 2 180.0 10 | 8 OS4 6 1.810 3 109.5 2 60.0 11 | 9 OS4 6 1.810 3 109.5 2 300.0 12 | 13 | il.ff 14 | -------------------------------------------------------------------------------- /c1c1im.zmat: -------------------------------------------------------------------------------- 1 | c1c1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 H1 8 1.090 3 109.5 4 60.0 17 | 15 H1 8 1.090 3 109.5 4 180.0 18 | 16 H1 8 1.090 3 109.5 4 300.0 19 | 20 | connect 5 1 21 | 22 | improper 5 2 1 6 23 | improper 1 3 2 7 24 | improper 2 4 3 8 25 | improper 3 5 4 9 26 | improper 4 1 5 10 27 | 28 | il.ff 29 | -------------------------------------------------------------------------------- /c1c1pyrr.zmat: -------------------------------------------------------------------------------- 1 | c1c1pyrr+ 2 | 3 | 1 N4 4 | 2 C1A 1 1.471 5 | 3 C1A 1 1.471 2 109.5 6 | 4 C2 2 1.529 1 109.5 3 0.0 7 | 5 C2 3 1.529 1 109.5 2 0.0 8 | 6 C1 1 1.471 2 109.5 3 120.0 9 | 7 C1 1 1.471 2 109.5 3 240.0 10 | 8 H1 2 1.090 1 109.5 6 0.0 11 | 9 H1 2 1.090 1 109.5 7 0.0 12 | 10 H1 3 1.090 1 109.5 6 0.0 13 | 11 H1 3 1.090 1 109.5 7 0.0 14 | 12 HC 4 1.090 2 110.7 8 0.0 15 | 13 HC 4 1.090 2 110.7 9 0.0 16 | 14 HC 5 1.090 3 110.7 10 0.0 17 | 15 HC 5 1.090 3 110.7 11 0.0 18 | 16 H1 6 1.090 1 109.5 2 60.0 19 | 17 H1 6 1.090 1 109.5 16 120.0 20 | 18 H1 6 1.090 1 109.5 16 240.0 21 | 19 H1 7 1.090 1 109.5 3 60.0 22 | 20 H1 7 1.090 1 109.5 19 120.0 23 | 21 H1 7 1.090 1 109.5 19 240.0 24 | 25 | connect 5 4 26 | 27 | il.ff 28 | -------------------------------------------------------------------------------- /c2OHc1im.zmat: -------------------------------------------------------------------------------- 1 | C2OHC1im 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 C2O 8 1.520 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 OH 14 1.090 8 109.5 3 180.0 20 | 18 HC 14 1.400 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 HO 17 0.950 14 109.5 8 180.0 23 | 24 | connect 5 1 25 | 26 | il.ff 27 | 28 | -------------------------------------------------------------------------------- /c2SO3.zmat: -------------------------------------------------------------------------------- 1 | ethylsulfonate 2 | 3 | 1 SO 4 | 2 OS3 1 1.455 5 | 3 OS3 1 1.455 2 109.5 6 | 4 OS3 1 1.455 2 109.5 3 120.0 7 | 5 CS3 1 1.792 2 109.5 3 240.0 8 | 6 CT 5 1.529 1 109.5 2 60.0 9 | 7 HS3 5 1.090 1 109.5 2 180.0 10 | 8 HS3 5 1.090 1 109.5 2 300.0 11 | 9 HC 6 1.529 5 109.5 1 60.0 12 | 10 HC 6 1.090 5 109.5 1 180.0 13 | 11 HC 6 1.090 5 109.5 1 300.0 14 | 15 | il.ff 16 | -------------------------------------------------------------------------------- /c2SO4.zmat: -------------------------------------------------------------------------------- 1 | ethylsulfate 2 | 3 | 1 CT 4 | 2 CS4 1 1.529 5 | 3 OC4 2 1.529 1 109.5 6 | 4 HC 1 1.090 2 109.5 3 180.0 7 | 5 HC 1 1.090 2 109.5 3 60.0 8 | 6 HC 1 1.090 2 109.5 3 -60.0 9 | 7 HS4 2 1.090 1 109.5 4 60.0 10 | 8 HS4 2 1.090 1 109.5 4 -60.0 11 | 9 SO 3 1.810 2 109.5 1 180.0 12 | 10 OS4 9 1.810 3 109.5 2 180.0 13 | 11 OS4 9 1.810 3 109.5 2 60.0 14 | 12 OS4 9 1.810 3 109.5 2 300.0 15 | 16 | il.ff 17 | -------------------------------------------------------------------------------- /c2c1c1im.zmat: -------------------------------------------------------------------------------- 1 | c2c1c1im+ 2 | 3 | 1 NAM 4 | 2 CRM 1 1.315 5 | 3 NAM 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 CCR 2 1.510 1 125.8 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 CE 8 1.529 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 HC 14 1.090 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 H1 7 1.090 2 109.5 1 0.0 23 | 21 H1 7 1.090 2 109.5 1 120.0 24 | 22 H1 7 1.090 2 109.5 1 240.0 25 | 26 | connect 5 1 27 | 28 | improper 5 2 1 6 29 | improper 1 3 2 7 30 | improper 2 4 3 8 31 | improper 3 5 4 9 32 | improper 4 1 5 10 33 | 34 | il.ff 35 | -------------------------------------------------------------------------------- /c2c1im.zmat: -------------------------------------------------------------------------------- 1 | c2c1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 CE 8 1.520 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 HC 14 1.090 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 23 | connect 5 1 24 | 25 | improper 5 2 1 6 26 | improper 1 3 2 7 27 | improper 2 4 3 8 28 | improper 3 5 4 9 29 | improper 4 1 5 10 30 | 31 | il.ff 32 | -------------------------------------------------------------------------------- /c2im.zmat: -------------------------------------------------------------------------------- 1 | c2im+ 2 | 3 | 1 NAH 4 | 2 CRH 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CWH 4 1.341 3 107.1 2 0.0 8 | 6 HCR 2 1.080 1 125.1 3 180.0 9 | 7 C1A 3 1.466 2 126.3 1 180.0 10 | 8 HCW 4 1.080 3 126.45 2 180.0 11 | 9 HCW 5 1.080 4 126.45 3 180.0 12 | 10 CE 7 1.520 3 109.5 2 0.0 13 | 11 H1 7 1.090 3 109.5 2 120.0 14 | 12 H1 7 1.090 3 109.5 2 240.0 15 | 13 HC 10 1.090 7 109.5 3 180.0 16 | 14 HC 10 1.090 7 109.5 3 300.0 17 | 15 HC 10 1.090 7 109.5 3 60.0 18 | 16 HNA 1 1.010 2 125.4 3 180.0 19 | 20 | connect 5 1 21 | 22 | improper 5 2 1 16 23 | improper 1 3 2 6 24 | improper 2 4 3 7 25 | improper 3 5 4 8 26 | improper 4 1 5 9 27 | 28 | il.ff -------------------------------------------------------------------------------- /c2o1mpyr.xyz: -------------------------------------------------------------------------------- 1 | 28 2 | C2O1mpyr+ il.ff 3 | C1A -0.73083 -0.17620 -1.20735 4 | C2 -0.50482 -1.51254 -0.51450 5 | C2 0.02177 -1.17008 0.86107 6 | HC -1.42108 -2.10897 -0.47004 7 | HC 0.24045 -2.09614 -1.06849 8 | C1A 0.91024 0.02463 0.59306 9 | HC -0.80021 -0.90490 1.53552 10 | HC 0.57260 -1.99997 1.31276 11 | N4 0.12374 0.85125 -0.44259 12 | H1 -0.40512 -0.21270 -2.25162 13 | H1 -1.77835 0.13794 -1.16237 14 | H1 1.11782 0.63826 1.47404 15 | H1 1.85213 -0.28993 0.12700 16 | C1 -0.77466 1.84850 0.29527 17 | H1 -1.45953 2.30687 -0.42219 18 | H1 -1.35653 1.30347 1.04429 19 | H1 -0.13974 2.59442 0.78060 20 | C1A 1.12605 1.59218 -1.35883 21 | OY 0.03779 3.72840 -1.74090 22 | H1 1.78877 2.15612 -0.69210 23 | H1 1.70338 0.81621 -1.87409 24 | C3O -0.34787 4.72772 -2.68293 25 | HY -0.69827 5.60396 -2.13116 26 | HY 0.50970 5.02155 -3.29611 27 | HY -1.15969 4.36194 -3.31859 28 | COM 0.47567 2.53222 -2.38864 29 | HC -0.37248 2.05811 -2.89291 30 | HC 1.23008 2.79120 -3.14059 31 | -------------------------------------------------------------------------------- /c2py.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | c2py+ il.ff 3 | NAP -0.47357 -0.07756 -0.17177 4 | CAPO 0.89335 -0.09544 -0.01718 5 | CAPO -1.20280 -1.20437 0.10335 6 | CAPM 1.54528 -1.25244 0.41795 7 | HAP 1.49820 0.77459 -0.22506 8 | CAPP 0.80433 -2.39640 0.69720 9 | HAP 2.62111 -1.25911 0.53728 10 | CAPM -0.57752 -2.37459 0.53975 11 | HAP 1.29993 -3.29747 1.03477 12 | HAP -1.16411 -3.25863 0.75403 13 | HAP -2.28041 -1.20012 -0.01541 14 | C1A -1.21726 1.11736 -0.62881 15 | CE -0.36504 2.35536 -0.92532 16 | HC 0.36005 2.14339 -1.73952 17 | HC 0.17155 2.68706 -0.01117 18 | HC -1.02455 3.18454 -1.25808 19 | H1 -1.95833 1.39741 0.15192 20 | H1 -1.77188 0.85950 -1.55782 21 | -------------------------------------------------------------------------------- /c3c1im.zmat: -------------------------------------------------------------------------------- 1 | c3c1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 C2 8 1.529 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 CT 14 1.529 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 HC 17 1.090 14 109.5 8 180.0 23 | 21 HC 17 1.090 14 109.5 8 60.0 24 | 22 HC 17 1.090 14 109.5 8 300.0 25 | 26 | connect 5 1 27 | 28 | improper 5 2 1 6 29 | improper 1 3 2 7 30 | improper 2 4 3 8 31 | improper 3 5 4 9 32 | improper 4 1 5 10 33 | 34 | il.ff 35 | -------------------------------------------------------------------------------- /c3c1pyrr.zmat: -------------------------------------------------------------------------------- 1 | c3c1pyrr+ 2 | 3 | 1 N4 4 | 2 C1A 1 1.471 5 | 3 C1A 1 1.471 2 109.5 6 | 4 C2 2 1.529 1 109.5 3 0.0 7 | 5 C2 3 1.529 1 109.5 2 0.0 8 | 6 C1 1 1.471 2 109.5 3 120.0 9 | 7 C1A 1 1.471 2 109.5 3 240.0 10 | 8 H1 2 1.090 1 109.5 6 0.0 11 | 9 H1 2 1.090 1 109.5 7 0.0 12 | 10 H1 3 1.090 1 109.5 6 0.0 13 | 11 H1 3 1.090 1 109.5 7 0.0 14 | 12 HC 4 1.090 2 110.7 8 0.0 15 | 13 HC 4 1.090 2 110.7 9 0.0 16 | 14 HC 5 1.090 3 110.7 10 0.0 17 | 15 HC 5 1.090 3 110.7 11 0.0 18 | 16 H1 6 1.090 1 109.5 2 60.0 19 | 17 H1 6 1.090 1 109.5 16 120.0 20 | 18 H1 6 1.090 1 109.5 16 240.0 21 | 19 H1 7 1.090 1 109.5 3 60.0 22 | 20 H1 7 1.090 1 109.5 19 120.0 23 | 21 C2 7 1.529 1 109.5 19 240.0 24 | 22 HC 21 1.090 7 109.5 1 60.0 25 | 23 HC 21 1.090 7 109.5 1 300.0 26 | 24 CT 21 1.529 7 109.5 1 180.0 27 | 25 HC 24 1.090 21 109.5 7 60.0 28 | 26 HC 24 1.090 21 109.5 7 300.0 29 | 27 HC 24 1.090 21 109.5 7 180.0 30 | 31 | connect 5 4 32 | 33 | il.ff 34 | -------------------------------------------------------------------------------- /c4c1c1im.zmat: -------------------------------------------------------------------------------- 1 | c4c1c1im+ 2 | 3 | 1 NAM 4 | 2 CRM 1 1.315 5 | 3 NAM 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 CCR 2 1.510 1 125.8 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 C2 8 1.529 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 CS 14 1.529 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 CT 17 1.529 14 109.5 8 180.0 23 | 21 HC 17 1.090 14 109.5 8 60.0 24 | 22 HC 17 1.090 14 109.5 8 300.0 25 | 23 HC 20 1.090 17 109.5 14 180.0 26 | 24 HC 20 1.090 17 109.5 14 60.0 27 | 25 HC 20 1.090 17 109.5 14 300.0 28 | 26 H1 7 1.090 2 109.5 1 0.0 29 | 27 H1 7 1.090 2 109.5 1 120.0 30 | 28 H1 7 1.090 2 109.5 1 240.0 31 | 32 | connect 5 1 33 | 34 | improper 5 2 1 6 35 | improper 1 3 2 7 36 | improper 2 4 3 8 37 | improper 3 5 4 9 38 | improper 4 1 5 10 39 | 40 | il.ff 41 | -------------------------------------------------------------------------------- /c4c1im.zmat: -------------------------------------------------------------------------------- 1 | c4c1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 C2 8 1.529 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 CS 14 1.529 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 CT 17 1.529 14 109.5 8 180.0 23 | 21 HC 17 1.090 14 109.5 8 60.0 24 | 22 HC 17 1.090 14 109.5 8 300.0 25 | 23 HC 20 1.090 17 109.5 14 180.0 26 | 24 HC 20 1.090 17 109.5 14 60.0 27 | 25 HC 20 1.090 17 109.5 14 300.0 28 | 29 | connect 5 1 30 | 31 | improper 2 5 1 6 32 | improper 1 3 2 7 33 | improper 2 4 3 8 34 | improper 3 5 4 9 35 | improper 1 4 5 10 36 | 37 | il.ff 38 | -------------------------------------------------------------------------------- /c4c1pyrr.zmat: -------------------------------------------------------------------------------- 1 | c4c1pyrr+ 2 | 3 | 1 N4 4 | 2 C1A 1 1.471 5 | 3 C1A 1 1.471 2 109.5 6 | 4 C2 2 1.529 1 109.5 3 0.0 7 | 5 C2 3 1.529 1 109.5 2 0.0 8 | 6 C1 1 1.471 2 109.5 3 120.0 9 | 7 C1A 1 1.471 2 109.5 3 240.0 10 | 8 H1 2 1.090 1 109.5 6 0.0 11 | 9 H1 2 1.090 1 109.5 7 0.0 12 | 10 H1 3 1.090 1 109.5 6 0.0 13 | 11 H1 3 1.090 1 109.5 7 0.0 14 | 12 HC 4 1.090 2 110.7 8 0.0 15 | 13 HC 4 1.090 2 110.7 9 0.0 16 | 14 HC 5 1.090 3 110.7 10 0.0 17 | 15 HC 5 1.090 3 110.7 11 0.0 18 | 16 H1 6 1.090 1 109.5 2 60.0 19 | 17 H1 6 1.090 1 109.5 16 120.0 20 | 18 H1 6 1.090 1 109.5 16 240.0 21 | 19 H1 7 1.090 1 109.5 3 60.0 22 | 20 H1 7 1.090 1 109.5 19 120.0 23 | 21 C2 7 1.529 1 109.5 19 240.0 24 | 22 HC 21 1.090 7 109.5 1 60.0 25 | 23 HC 21 1.090 7 109.5 1 300.0 26 | 24 CS 21 1.529 7 109.5 1 180.0 27 | 25 HC 24 1.090 21 109.5 7 60.0 28 | 26 HC 24 1.090 21 109.5 7 300.0 29 | 27 CT 24 1.529 21 109.5 7 180.0 30 | 28 HC 27 1.090 24 109.5 21 60.0 31 | 29 HC 27 1.090 24 109.5 21 300.0 32 | 30 HC 27 1.090 24 109.5 21 180.0 33 | 34 | connect 5 4 35 | 36 | il.ff 37 | -------------------------------------------------------------------------------- /c4c4im.zmat: -------------------------------------------------------------------------------- 1 | c4c4im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1A 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 C2 8 1.529 3 109.5 4 180.0 14 | 12 H1 8 1.090 3 109.5 11 120.0 15 | 13 H1 8 1.090 3 109.5 11 240.0 16 | 14 CS 11 1.529 8 109.5 3 180.0 17 | 15 HC 11 1.090 8 109.5 14 120.0 18 | 16 HC 11 1.090 8 109.5 14 240.0 19 | 17 CT 14 1.529 11 109.5 8 180.0 20 | 18 HC 14 1.090 11 109.5 8 60.0 21 | 19 HC 14 1.090 11 109.5 8 300.0 22 | 20 HC 17 1.090 14 109.5 11 180.0 23 | 21 HC 17 1.090 14 109.5 11 60.0 24 | 22 HC 17 1.090 14 109.5 11 300.0 25 | 23 C2 6 1.529 1 109.5 5 180.0 26 | 24 H1 6 1.090 1 109.5 23 120.0 27 | 25 H1 6 1.090 1 109.5 23 240.0 28 | 26 CS 23 1.529 6 109.5 1 180.0 29 | 27 HC 23 1.090 6 109.5 26 120.0 30 | 28 HC 23 1.090 6 109.5 26 240.0 31 | 29 CT 26 1.529 23 109.5 6 180.0 32 | 30 HC 26 1.090 23 109.5 29 120.0 33 | 31 HC 26 1.090 23 109.5 29 240.0 34 | 32 HC 29 1.090 26 109.5 23 180.0 35 | 33 HC 29 1.090 26 109.5 23 60.0 36 | 34 HC 29 1.090 26 109.5 23 300.0 37 | 38 | connect 5 1 39 | 40 | improper 5 2 1 6 41 | improper 1 3 2 7 42 | improper 2 4 3 8 43 | improper 3 5 4 9 44 | improper 4 1 5 10 45 | 46 | il.ff 47 | -------------------------------------------------------------------------------- /c4fc1fsi.zmat: -------------------------------------------------------------------------------- 1 | 41si- 2 | 3 | 1 CBT 4 | 2 F1 1 1.332 5 | 3 F1 1 1.332 2 107.1 6 | 4 F1 1 1.332 2 107.1 3 120.0 7 | 5 SBT 1 1.818 2 111.8 3 -120.0 8 | 6 NBT 5 1.700 1 102.6 3 60.0 9 | 7 OBT 5 1.443 1 102.6 6 120.0 10 | 8 OBT 5 1.443 1 102.6 6 -120.0 11 | 9 SBT 6 1.700 5 120.0 1 90.0 12 | 10 OBT 9 1.443 6 102.6 5 -30.0 13 | 11 OBT 9 1.443 6 102.6 5 -150.0 14 | 12 C1F 9 1.818 6 102.6 5 90.0 15 | 13 CSF 12 1.529 9 111.8 6 180.0 16 | 14 F1 12 1.332 9 107.1 13 120.0 17 | 15 F1 12 1.332 9 107.1 13 240.0 18 | 16 CSF 13 1.529 12 109.5 9 180.0 19 | 17 F 13 1.332 12 107.1 16 120.0 20 | 18 F 13 1.332 12 107.1 16 240.0 21 | 19 CTF 16 1.529 13 109.5 12 180.0 22 | 20 F 16 1.332 13 109.5 12 -60.0 23 | 21 F 16 1.332 13 109.5 12 60.0 24 | 22 F 19 1.332 16 109.5 13 180.0 25 | 23 F 19 1.332 16 109.5 13 60.0 26 | 24 F 19 1.332 16 109.5 13 -60.0 27 | 28 | il.ff 29 | -------------------------------------------------------------------------------- /c4pyri.zmat: -------------------------------------------------------------------------------- 1 | # molecule name (max 15 chars) 2 | bpyri+ 3 | 4 | # Z-matrix (atom labels max 3 chars) 5 | 1 NAP 6 | 2 CAPO 1 1.365 7 | 3 CAPM 2 1.400 1 120.0 8 | 4 CAPP 3 1.400 2 120.0 1 0.0 9 | 5 CAPM 4 1.400 3 120.0 2 0.0 10 | 6 CAPO 5 1.400 4 120.0 3 0.0 11 | 7 C1A 1 1.475 2 119.8 3 180.0 12 | 8 HAP 2 1.08 1 126.0 6 180.0 13 | 9 HAP 3 1.08 2 126.45 1 180.0 14 | 10 HAP 4 1.08 3 126.45 2 180.0 15 | 11 HAP 5 1.08 4 109.5 3 180.0 16 | 12 HAP 6 1.08 5 109.5 4 180.0 17 | 13 C2 7 1.529 1 109.5 2 90.0 18 | 14 H1 7 1.09 1 109.5 13 120.0 19 | 15 H1 7 1.09 1 109.5 13 240.0 20 | 16 CS 13 1.529 7 109.5 1 180.0 21 | 17 HC 13 1.09 7 109.5 16 120.0 22 | 18 HC 13 1.09 7 109.5 16 240.0 23 | 19 CT 16 1.529 13 109.5 7 180.0 24 | 20 HC 16 1.09 13 109.5 19 120.0 25 | 21 HC 16 1.09 13 109.5 19 240.0 26 | 22 HC 19 1.09 16 109.5 13 180.0 27 | 23 HC 19 1.09 16 109.5 22 120.0 28 | 24 HC 19 1.09 16 109.5 22 240.0 29 | 30 | connect 6 1 31 | 32 | # site parameters: m/uma, q/e, field, sig/A, eps/kJmol, dummy 33 | il.ff 34 | -------------------------------------------------------------------------------- /c6c1im.zmat: -------------------------------------------------------------------------------- 1 | c6c1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 C2 8 1.529 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 CS 14 1.529 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 CS 17 1.529 14 109.5 8 180.0 23 | 21 HC 17 1.090 14 109.5 8 60.0 24 | 22 HC 17 1.090 14 109.5 8 300.0 25 | 23 CS 20 1.529 17 109.5 14 180.0 26 | 24 HC 20 1.090 17 109.5 14 60.0 27 | 25 HC 20 1.090 17 109.5 14 300.0 28 | 26 CT 23 1.529 20 109.5 17 180.0 29 | 27 HC 23 1.090 20 109.5 17 60.0 30 | 28 HC 23 1.090 20 109.5 17 300.0 31 | 29 HC 26 1.090 23 109.5 20 180.0 32 | 30 HC 26 1.090 23 109.5 20 60.0 33 | 31 HC 26 1.090 23 109.5 20 300.0 34 | 35 | connect 5 1 36 | 37 | improper 5 2 1 6 38 | improper 1 3 2 7 39 | improper 2 4 3 8 40 | improper 3 5 4 9 41 | improper 4 1 5 10 42 | 43 | il.ff 44 | -------------------------------------------------------------------------------- /c8c1im.zmat: -------------------------------------------------------------------------------- 1 | c8c1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1A 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 C2 8 1.529 3 109.5 4 180.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 CS 14 1.529 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 CS 17 1.529 14 109.5 8 180.0 23 | 21 HC 17 1.090 14 109.5 8 60.0 24 | 22 HC 17 1.090 14 109.5 8 300.0 25 | 23 CS 20 1.529 17 109.5 14 180.0 26 | 24 HC 20 1.090 17 109.5 14 60.0 27 | 25 HC 20 1.090 17 109.5 14 300.0 28 | 26 CS 23 1.529 20 109.5 17 180.0 29 | 27 HC 23 1.090 20 109.5 17 60.0 30 | 28 HC 23 1.090 20 109.5 17 300.0 31 | 29 CS 26 1.529 23 109.5 20 180.0 32 | 30 HC 26 1.090 23 109.5 20 60.0 33 | 31 HC 26 1.090 23 109.5 20 300.0 34 | 32 CT 29 1.529 26 109.5 23 180.0 35 | 33 HC 29 1.090 26 109.5 23 60.0 36 | 34 HC 29 1.090 26 109.5 23 300.0 37 | 35 HC 32 1.090 29 109.5 26 180.0 38 | 36 HC 32 1.090 29 109.5 26 60.0 39 | 37 HC 32 1.090 29 109.5 26 300.0 40 | 41 | connect 5 1 42 | 43 | improper 5 2 1 6 44 | improper 1 3 2 7 45 | improper 2 4 3 8 46 | improper 3 5 4 9 47 | improper 4 1 5 10 48 | 49 | il.ff 50 | -------------------------------------------------------------------------------- /c8fc1im.zmat: -------------------------------------------------------------------------------- 1 | c8(f6)c1im+ 2 | 3 | 1 NA 4 | 2 CR 1 1.315 5 | 3 NA 2 1.315 1 109.8 6 | 4 CW 3 1.378 2 108.0 1 0.0 7 | 5 CW 4 1.341 3 107.1 2 0.0 8 | 6 C1 1 1.466 5 125.6 4 180.0 9 | 7 HCR 2 1.080 1 125.1 3 180.0 10 | 8 C1H 3 1.466 2 126.3 1 180.0 11 | 9 HCW 4 1.080 3 126.45 2 180.0 12 | 10 HCW 5 1.080 4 126.45 3 180.0 13 | 11 H1 6 1.090 1 109.5 5 60.0 14 | 12 H1 6 1.090 1 109.5 5 180.0 15 | 13 H1 6 1.090 1 109.5 5 300.0 16 | 14 C2 8 1.529 3 109.5 4 0.0 17 | 15 H1 8 1.090 3 109.5 14 120.0 18 | 16 H1 8 1.090 3 109.5 14 240.0 19 | 17 CFH 14 1.529 8 109.5 3 180.0 20 | 18 HC 14 1.090 8 109.5 17 120.0 21 | 19 HC 14 1.090 8 109.5 17 240.0 22 | 20 CSF 17 1.529 14 109.5 8 180.0 23 | 21 F 17 1.330 14 109.5 8 60.0 24 | 22 F 17 1.330 14 109.5 8 300.0 25 | 23 CSF 20 1.529 17 109.5 14 180.0 26 | 24 F 20 1.330 17 109.5 14 60.0 27 | 25 F 20 1.330 17 109.5 14 300.0 28 | 26 CSF 23 1.529 20 109.5 17 180.0 29 | 27 F 23 1.330 20 109.5 17 60.0 30 | 28 F 23 1.330 20 109.5 17 300.0 31 | 29 CSF 26 1.529 23 109.5 20 180.0 32 | 30 F 26 1.330 23 109.5 20 60.0 33 | 31 F 26 1.330 23 109.5 20 300.0 34 | 32 CTF 29 1.529 26 109.5 23 180.0 35 | 33 F 29 1.330 26 109.5 23 60.0 36 | 34 F 29 1.330 26 109.5 23 300.0 37 | 35 F 32 1.330 29 109.5 26 180.0 38 | 36 F 32 1.330 29 109.5 26 60.0 39 | 37 F 32 1.330 29 109.5 26 300.0 40 | 41 | connect 5 1 42 | 43 | improper 5 2 1 6 44 | improper 1 3 2 7 45 | improper 2 4 3 8 46 | improper 3 5 4 9 47 | improper 4 1 5 10 48 | 49 | il.ff 50 | -------------------------------------------------------------------------------- /c8isoqui.xyz: -------------------------------------------------------------------------------- 1 | 42 2 | c8isoqui il.ff 3 | NAQ -0.74629 -0.51020 0.00043 4 | CA -1.95481 -1.15466 -0.00308 5 | CAQ -3.15854 -0.43564 -0.00083 6 | CA -4.39779 -1.09509 -0.00359 7 | CA -5.58454 -0.35533 -0.00142 8 | CA -5.54213 1.04189 0.00324 9 | CA -4.31296 1.70746 0.00609 10 | CAQ -3.11682 0.97350 0.00431 11 | CA -1.87995 1.61895 0.00770 12 | CA -0.70617 0.86397 0.00611 13 | HAP -1.98773 -2.23971 -0.00736 14 | HA -4.44861 -2.17730 -0.00725 15 | HA -6.53897 -0.86563 -0.00341 16 | HA -6.46327 1.61020 0.00475 17 | HA -4.29698 2.79094 0.00978 18 | HAP -1.81785 2.70088 0.01165 19 | HAP 0.22509 1.41034 0.00896 20 | C1A 0.46484 -1.36195 -0.00281 21 | H1 0.43803 -2.02021 0.89416 22 | H1 0.44206 -2.00635 -0.90987 23 | C2 1.79770 -0.59371 0.00785 24 | CS 3.00029 -1.54483 -0.00250 25 | CS 4.30960 -0.74682 0.01501 26 | CS 5.53292 -1.66923 -0.00782 27 | CS 6.82722 -0.84678 0.01317 28 | CS 8.06233 -1.75267 -0.01912 29 | CT 9.34618 -0.92767 0.00340 30 | HC 1.84843 0.03405 0.92471 31 | HC 1.85303 0.05456 -0.89429 32 | HC 2.96344 -2.17594 -0.91782 33 | HC 2.95902 -2.20613 0.89105 34 | HC 4.34170 -0.11972 0.93353 35 | HC 4.34202 -0.07913 -0.87439 36 | HC 5.50606 -2.29208 -0.92913 37 | HC 5.50719 -2.33974 0.87943 38 | HC 6.85165 -0.22658 0.93661 39 | HC 6.84686 -0.17177 -0.87109 40 | HC 8.04829 -2.37042 -0.94348 41 | HC 8.05395 -2.42902 0.86326 42 | HC 9.38877 -0.25534 -0.88008 43 | HC 10.22549 -1.60494 -0.02251 44 | HC 9.39547 -0.31568 0.92934 45 | -------------------------------------------------------------------------------- /chexoat.xyz: -------------------------------------------------------------------------------- 1 | 20 2 | chexanoat il.ff 3 | CO2 0.00000 0.00000 0.00000 4 | O2 1.21404 0.00763 -0.02079 5 | O2 -0.68410 -0.79017 0.78770 6 | C3C -0.85180 0.90139 -0.88076 7 | CT2 -1.71874 1.86827 -0.03517 8 | HC -1.07467 2.47384 0.60715 9 | HC -2.38838 1.30075 0.61639 10 | CT2 -2.55758 2.79424 -0.94315 11 | CT2 -1.73853 0.07768 -1.84857 12 | HC -0.16857 1.50525 -1.48447 13 | HC -2.40910 -0.57370 -1.28193 14 | HC -1.10825 -0.56387 -2.46926 15 | CT2 -2.57734 1.00647 -2.75370 16 | HC -3.22456 0.40526 -3.39672 17 | HC -1.91428 1.58166 -3.40512 18 | HC -1.89368 3.44565 -1.51738 19 | HC -3.19105 3.43658 -0.32677 20 | CT2 -3.43763 1.97051 -1.90820 21 | HC -3.98938 2.64459 -2.56778 22 | HC -4.17368 1.39943 -1.33627 23 | -------------------------------------------------------------------------------- /cholinium.xyz: -------------------------------------------------------------------------------- 1 | 21 2 | cholinium des.ff 3 | N4 -2.76844 0.42637 -0.33761 4 | C1 -1.28508 0.43893 -0.33929 5 | C1 -3.23170 0.55081 1.06513 6 | C1 -3.22189 -0.87046 -0.89473 7 | H1 -2.92786 1.52841 1.50158 8 | H1 -2.80231 -0.25615 1.70079 9 | H1 -4.33530 0.45819 1.14380 10 | H1 -0.89034 1.38981 0.08472 11 | H1 -0.88302 0.33341 -1.37224 12 | H1 -0.87136 -0.39705 0.26899 13 | H1 -2.90943 -0.98071 -1.95714 14 | H1 -4.32548 -0.97871 -0.83967 15 | H1 -2.79307 -1.72330 -0.32163 16 | C1A -3.23844 1.57500 -1.17308 17 | H1 -2.83844 2.52855 -0.75687 18 | COL -4.76723 1.73417 -1.29332 19 | H1 -2.83356 1.47587 -2.20689 20 | HC -5.21476 1.90282 -0.29129 21 | HC -5.21093 0.83260 -1.76549 22 | OH -5.04432 2.84487 -2.10056 23 | HO -6.03341 2.91557 -2.14578 24 | -------------------------------------------------------------------------------- /dca.zmat: -------------------------------------------------------------------------------- 1 | dca- 2 | 3 | 1 N3A 4 | 2 CZA 1 1.310 5 | 3 NZA 2 1.150 1 175.2 6 | 4 CZA 1 1.310 2 118.5 3 180.0 7 | 5 NZA 4 1.150 1 175.2 2 180.0 8 | 9 | il.ff 10 | -------------------------------------------------------------------------------- /fsi.zmat: -------------------------------------------------------------------------------- 1 | fsi- 2 | 3 | 1 FSI 4 | 2 SBT 1 1.575 5 | 3 NBT 2 1.500 1 103.0 6 | 4 OBT 2 1.443 1 104.1 3 120.0 7 | 5 OBT 2 1.443 1 104.1 3 -120.0 8 | 6 SBT 3 1.500 2 120.0 1 90.0 9 | 7 OBT 6 1.443 3 102.6 2 -30.0 10 | 8 OBT 6 1.443 3 102.6 2 -150.0 11 | 9 FSI 6 1.575 3 103.0 2 90.0 12 | 13 | il.ff 14 | -------------------------------------------------------------------------------- /gua.zmat: -------------------------------------------------------------------------------- 1 | guanidinium 2 | 3 | CG 4 | NG 1 1.34 5 | NG 1 1.34 2 120.0 6 | NG 1 1.34 2 120.0 3 180.0 7 | HG 2 1.01 1 120.0 3 0.0 8 | HG 2 1.01 1 120.0 3 180.0 9 | HG 4 1.01 1 120.0 2 360.0 10 | HG 4 1.01 1 120.0 2 180.0 11 | HG 3 1.01 1 120.0 2 360.0 12 | HG 3 1.01 1 120.0 2 180.0 13 | 14 | il.ff 15 | -------------------------------------------------------------------------------- /ilff_structures.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paduagroup/clandp/f0c4b3e05d195df3ff320c9f263e26ffa2536e51/ilff_structures.pdf -------------------------------------------------------------------------------- /isoval.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | isovalerate il.ff 3 | CO2 -0.85526 0.10933 -0.81906 4 | O2 -0.24187 0.44638 -1.81143 5 | O2 -1.04221 0.90542 0.20115 6 | C2C -1.29693 -1.31696 -0.55256 7 | CT3 -0.26352 -2.12281 0.27755 8 | HC -1.48300 -1.81666 -1.50658 9 | HC -2.24983 -1.29257 -0.01703 10 | CT 1.08501 -2.26813 -0.46426 11 | CT -0.82926 -3.51952 0.61517 12 | HC -0.08372 -1.59529 1.21801 13 | HC -1.02393 -4.09178 -0.29530 14 | HC -1.76458 -3.43183 1.17306 15 | HC -0.12250 -4.08222 1.22974 16 | HC 0.94618 -2.74693 -1.43659 17 | HC 1.78019 -2.87495 0.12072 18 | HC 1.55120 -1.29325 -0.62291 19 | -------------------------------------------------------------------------------- /ntf2.zmat: -------------------------------------------------------------------------------- 1 | tf2N- 2 | 3 | 1 CBT 4 | 2 F1 1 1.332 5 | 3 F1 1 1.332 2 107.1 6 | 4 F1 1 1.332 2 107.1 3 120.0 7 | 5 SBT 1 1.818 2 111.8 3 -120.0 8 | 6 NBT 5 1.700 1 102.6 3 60.0 9 | 7 OBT 5 1.443 1 102.6 6 120.0 10 | 8 OBT 5 1.443 1 102.6 6 -120.0 11 | 9 SBT 6 1.700 5 120.0 1 90.0 12 | 10 OBT 9 1.443 6 102.6 5 -30.0 13 | 11 OBT 9 1.443 6 102.6 5 -150.0 14 | 12 CBT 9 1.818 6 102.6 5 90.0 15 | 13 F1 12 1.332 9 107.1 6 60.0 16 | 14 F1 12 1.332 9 107.1 6 -60.0 17 | 15 F1 12 1.332 9 107.1 6 180.0 18 | 19 | il.ff 20 | -------------------------------------------------------------------------------- /oac.zmat: -------------------------------------------------------------------------------- 1 | acetate 2 | 3 | 1 CTA 4 | 2 HC 1 1.090 5 | 3 HC 1 1.090 2 109.5 6 | 4 HC 1 1.090 2 109.5 3 120.0 7 | 5 CO2 1 1.522 2 120.0 3 -120.0 8 | 6 O2 5 1.255 1 110.0 3 60.0 9 | 7 O2 5 1.255 1 117.0 6 180.0 10 | 11 | il.ff 12 | -------------------------------------------------------------------------------- /otf.zmat: -------------------------------------------------------------------------------- 1 | otf- 2 | 3 | 1 CBT 4 | 2 F1 1 rCF 5 | 3 F1 1 rCF 2 107.1 6 | 4 F1 1 rCF 2 107.1 3 120.0 7 | 5 SBT 1 rCS 2 111.8 3 -120.0 8 | 6 OTF 5 rSO 1 102.6 3 60.0 9 | 7 OTF 5 rSO 1 102.6 6 120.0 10 | 8 OTF 5 rSO 1 102.6 6 -120.0 11 | 12 | rCF = 1.332 13 | rSO = 1.443 14 | rCS = 1.818 15 | 16 | il.ff 17 | -------------------------------------------------------------------------------- /phoac.zmat: -------------------------------------------------------------------------------- 1 | Phoac 2 | 3 | CO2 4 | O2 1 1.256 5 | O2 1 1.249 2 130.607 6 | C2C 1 1.602 2 114.693 3 177.1 7 | CPH 4 1.503 1 115.519 2 53.9 8 | HC 4 1.101 1 104.985 2 293.8 9 | HC 4 1.095 1 109.033 2 178.7 10 | CAO 5 1.409 4 121.027 1 304.9 11 | CAO 5 1.405 4 121.465 1 124.5 12 | CAM 8 1.393 5 120.959 4 180.2 13 | HA 8 1.085 5 117.099 4 3.6 14 | CAM 9 1.397 5 121.621 4 179.8 15 | HA 9 1.089 5 118.820 4 359.9 16 | CAP 12 1.396 9 120.165 5 0.0 17 | HA 12 1.089 9 119.740 5 180.1 18 | HA 14 1.089 12 120.498 9 180.2 19 | HA 10 1.089 8 119.488 5 180.3 20 | 21 | connect 14 10 22 | 23 | improper 8 9 5 4 24 | improper 5 10 8 11 25 | improper 8 14 10 17 26 | improper 10 12 14 16 27 | improper 9 14 12 15 28 | improper 5 12 9 13 29 | 30 | il.ff 31 | 32 | -------------------------------------------------------------------------------- /pmbzoat.xyz: -------------------------------------------------------------------------------- 1 | 17 2 | pmbzoat il.ff 3 | CO2 0.00000 0.00000 0.00000 4 | O2 -0.57723 1.06985 0.00000 5 | O2 -0.57722 -1.06985 -0.00000 6 | CBI 1.50558 -0.00000 -0.00000 7 | CAO 2.21910 1.20322 -0.00000 8 | CAO 2.21904 -1.20321 -0.00000 9 | HA 1.68708 2.15102 -0.00001 10 | CAM 3.61313 1.20399 -0.00001 11 | CAM 3.61297 -1.20335 -0.00001 12 | CBP 4.31839 -0.00013 -0.00000 13 | HA 1.68722 -2.15112 -0.00001 14 | HA 4.14435 2.15190 -0.00002 15 | CT 5.83641 -0.01080 -0.00003 16 | HA 4.14696 -2.14978 -0.00002 17 | HC 6.23959 1.00430 0.00144 18 | HC 6.21128 -0.52638 -0.88685 19 | HC 6.21132 -0.52893 0.88529 20 | -------------------------------------------------------------------------------- /tfa.zmat: -------------------------------------------------------------------------------- 1 | trifluoroacetate 2 | 3 | 1 CFA 4 | 2 FFA 1 1.332 5 | 3 FFA 1 1.332 2 109.5 6 | 4 FFA 1 1.332 2 109.5 3 120.0 7 | 5 CO2 1 1.529 2 120.0 3 -120.0 8 | 6 O2F 5 1.250 1 110.0 3 60.0 9 | 7 O2F 5 1.250 1 117.0 6 180.0 10 | 11 | il.ff 12 | -------------------------------------------------------------------------------- /topologies/README.md: -------------------------------------------------------------------------------- 1 | Gromacs topology files for ionic liquids 2 | ======================================== 3 | 4 | _Vitaly Chaban_ 5 | 6 | Contents 7 | ---- 8 | 9 | Input files in Gromacs format. This version of the force field has been refined for a better representation of transport properties. 10 | 11 | * `bpy*`: topology files for N-butyl-pyridinium ionic liquids with 12 | several anions. 13 | 14 | * `py14*`: topology files for N,N-butyl-methylpyrrolidinium ionic liquids with several anions. 15 | 16 | 17 | References 18 | ---- 19 | 20 | * I.V. Voroshylova, V.V. Chaban, J Phys Chem B 118 (2014) 10716-24, DOI: 21 | [10.1021/jp5054875](http://dx.doi.org/10.1021/jp5054875) 22 | 23 | * V.V. Chaban, I.V. Voroshylova, J Phys Chem B 119 (2015) 6242-9, DOI: 24 | [10.1021/jp5122678](http://dx.doi.org/10.1021/jp5122678) 25 | -------------------------------------------------------------------------------- /topologies/bpybf4/bf4.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BF4 2 3 | 4 | [ atoms ] 5 | 1 B 1 BF4 B1 1 0.84 10.8100 6 | 2 FB 1 BF4 F2 2 -0.42 18.9984 7 | 3 FB 1 BF4 F3 3 -0.42 18.9984 8 | 4 FB 1 BF4 F4 4 -0.42 18.9984 9 | 5 FB 1 BF4 F5 5 -0.42 18.9984 10 | 11 | [ bonds ] 12 | 1 2 1 13 | 1 3 1 14 | 1 4 1 15 | 1 5 1 16 | 17 | 18 | [ angles ] 19 | 2 1 3 1 20 | 2 1 4 1 21 | 2 1 5 1 22 | 3 1 5 1 23 | 3 1 4 1 24 | 4 1 5 1 25 | 26 | 27 | -------------------------------------------------------------------------------- /topologies/bpybf4/bpy.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BPY 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CA 1 BPY C1 0 -0.0588 12.011 7 | 2 CA 1 BPY C2 1 0.0000 12.011 8 | 3 NA 1 BPY N3 2 0.1260 14.0067 9 | 4 CA 1 BPY C4 3 0.0000 12.011 10 | 5 CA 1 BPY C5 4 -0.0588 12.011 11 | 6 HA 1 BPY H6 5 0.1260 1.008 12 | 7 HA 1 BPY H7 6 0.1260 1.008 13 | 8 HA 1 BPY H8 7 0.1260 1.008 14 | 9 HA 1 BPY H9 8 0.1260 1.008 15 | 10 CA 1 BPY C10 9 0.0168 12.011 16 | 11 HA 1 BPY H11 10 0.1260 1.008 17 | 12 CT 1 BPY C12 11 -0.1428 12.011 18 | 13 HC 1 BPY H13 12 0.1092 1.008 19 | 14 HC 1 BPY H14 13 0.1092 1.008 20 | 15 CT 1 BPY C15 14 0.0084 12.011 21 | 16 HC 1 BPY H16 15 0.0504 1.008 22 | 17 HC 1 BPY H17 16 0.0504 1.008 23 | 18 CT 1 BPY C18 17 -0.12 12.011 24 | 19 HC 1 BPY H19 18 0.06 1.008 25 | 20 HC 1 BPY H20 19 0.06 1.008 26 | 21 CT 1 BPY C21 20 -0.18 12.011 27 | 22 HC 1 BPY H22 21 0.06 1.008 28 | 23 HC 1 BPY H23 22 0.06 1.008 29 | 24 HC 1 BPY H24 23 0.06 1.008 30 | 31 | [ bonds ] 32 | 1 2 1 33 | 1 6 1 34 | 1 10 1 35 | 2 3 1 36 | 2 7 1 37 | 3 4 1 38 | 3 12 1 39 | 4 5 1 40 | 4 8 1 41 | 5 9 1 42 | 5 10 1 43 | 10 11 1 44 | 12 13 1 45 | 12 14 1 46 | 12 15 1 47 | 15 16 1 48 | 15 17 1 49 | 15 18 1 50 | 18 19 1 51 | 18 20 1 52 | 18 21 1 53 | 21 22 1 54 | 21 23 1 55 | 21 24 1 56 | 57 | [ pairs ] 58 | ; ai aj funct 59 | 1 4 1 60 | 1 9 1 61 | 1 12 1 62 | 2 5 1 63 | 2 8 1 64 | 2 11 1 65 | 2 13 1 66 | 2 14 1 67 | 2 15 1 68 | 3 6 1 69 | 3 9 1 70 | 3 10 1 71 | 3 16 1 72 | 3 17 1 73 | 3 18 1 74 | 4 7 1 75 | 4 11 1 76 | 4 13 1 77 | 4 14 1 78 | 4 15 1 79 | 5 6 1 80 | 5 12 1 81 | 6 7 1 82 | 6 11 1 83 | 7 10 1 84 | 7 12 1 85 | 8 9 1 86 | 8 10 1 87 | 8 12 1 88 | 9 11 1 89 | 12 19 1 90 | 12 20 1 91 | 12 21 1 92 | 13 16 1 93 | 13 17 1 94 | 13 18 1 95 | 14 16 1 96 | 14 17 1 97 | 14 18 1 98 | 15 22 1 99 | 15 23 1 100 | 15 24 1 101 | 16 19 1 102 | 16 20 1 103 | 16 21 1 104 | 17 19 1 105 | 17 20 1 106 | 17 21 1 107 | 19 22 1 108 | 19 23 1 109 | 19 24 1 110 | 20 22 1 111 | 20 23 1 112 | 20 24 1 113 | 114 | [ angles ] 115 | ; ai aj ak funct 116 | 2 1 6 1 117 | 2 1 10 1 118 | 6 1 10 1 119 | 1 2 3 1 120 | 1 2 7 1 121 | 3 2 7 1 122 | 2 3 4 1 123 | 2 3 12 1 124 | 4 3 12 1 125 | 3 4 5 1 126 | 3 4 8 1 127 | 5 4 8 1 128 | 4 5 9 1 129 | 4 5 10 1 130 | 9 5 10 1 131 | 1 10 5 1 132 | 1 10 11 1 133 | 5 10 11 1 134 | 3 12 13 1 135 | 3 12 14 1 136 | 3 12 15 1 137 | 13 12 14 1 138 | 13 12 15 1 139 | 14 12 15 1 140 | 12 15 16 1 141 | 12 15 17 1 142 | 12 15 18 1 143 | 16 15 17 1 144 | 16 15 18 1 145 | 17 15 18 1 146 | 15 18 19 1 147 | 15 18 20 1 148 | 15 18 21 1 149 | 19 18 20 1 150 | 19 18 21 1 151 | 20 18 21 1 152 | 18 21 22 1 153 | 18 21 23 1 154 | 18 21 24 1 155 | 22 21 23 1 156 | 22 21 24 1 157 | 23 21 24 1 158 | 159 | [ dihedrals ] 160 | ;CA-CA-CA-CA 161 | 2 1 10 5 5 162 | 1 10 5 4 5 163 | ;NA-CA-CA-CA 164 | 10 1 2 3 5 165 | 10 5 4 3 5 166 | ;HA-CA-CA-NA 167 | 6 1 2 3 5 168 | 9 5 4 3 5 169 | ;HA-CA-CA-HA 170 | 7 2 1 6 5 171 | 6 1 10 11 5 172 | 9 5 10 11 5 173 | 8 4 5 9 5 174 | ;CA-NA-CA-HA 175 | 2 3 4 8 5 176 | 4 3 2 7 5 177 | ;CT-NA-CA-HA 178 | 12 3 2 7 5 179 | 12 3 4 8 5 180 | ;CA-NA-CA-CA 181 | 2 3 4 5 5 182 | 4 3 2 1 5 183 | ;CT-NA-CA-CA 184 | 12 3 2 1 5 185 | 12 3 4 5 5 186 | ;HC-CT-NA-CA 187 | 13 12 3 2 5 188 | 14 12 3 2 5 189 | 13 12 3 4 5 190 | 14 12 3 4 5 191 | ;CT-CT-NA-CA 192 | 15 12 3 2 5 193 | 15 12 3 4 5 194 | ;NA-CT-CT-CT 195 | 3 12 15 18 5 196 | ;CT-CT-CT-CT 197 | 12 15 18 21 5 198 | ;HC-CT-CT-HC 199 | 13 12 15 16 5 200 | 14 12 15 16 5 201 | 13 12 15 17 5 202 | 14 12 15 18 5 203 | 16 15 18 19 5 204 | 17 15 18 19 5 205 | 16 15 18 20 5 206 | 17 15 18 20 5 207 | 19 18 21 22 5 208 | 19 18 21 23 5 209 | 19 18 21 24 5 210 | 20 18 21 22 5 211 | 20 18 21 23 5 212 | 20 18 21 24 5 213 | ;HC-CT-CT-CT 214 | 13 12 15 18 5 215 | 14 12 15 18 5 216 | 16 15 18 21 5 217 | 17 15 18 21 5 218 | 12 15 18 19 5 219 | 12 15 18 20 5 220 | 15 18 21 22 5 221 | 15 18 21 23 5 222 | 15 18 21 24 5 223 | ;improper dihedrals 224 | ;CA-CA-CA-HA 225 | 5 10 4 9 5 226 | 10 1 5 11 5 227 | 1 2 10 6 5 228 | ;CA-CA-NA-HA 229 | 4 5 3 8 5 230 | 2 3 1 7 5 231 | ;NA-CA-CA-CT 232 | 3 4 2 12 5 233 | -------------------------------------------------------------------------------- /topologies/bpybf4/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ; pyridinium 7 | NA 7 14.007 0.15 A 0.325 0.71128 8 | CA 6 12.011 0.00 A 0.355 0.29288 9 | HA 1 1.008 0.15 A 0.242 0.12552 10 | CT 6 12.011 -0.18 A 0.350 0.27614 11 | HC 1 1.008 0.06 A 0.250 0.12552 12 | 13 | ; tetrafluoroborate 14 | B 5 10.811 0.96 A 0.358 0.3975 15 | FB 9 18.998 -0.49 A 0.312 0.2552 16 | 17 | ; !!! 18 | [ nonbond_params ] 19 | FB HC 1 0.20 0.18 20 | 21 | [ bondtypes ] 22 | NA CT 1 0.1466 282000 23 | HC CT 1 0.1090 -284500 24 | CT CT 1 0.1529 224200 25 | NA HA 1 0.1010 -363200 26 | CA HA 1 0.1080 -307100 27 | CA CA 1 0.1380 392500 28 | CA NA 1 0.1340 404200 29 | 30 | B FB 1 0.1394 323500 31 | 32 | [ angletypes ] 33 | CT CT CT 1 112.7 488.3 34 | CT CT HC 1 110.7 313.8 35 | HC CT HC 1 107.8 276.1 36 | NA CT CT 1 112.7 488.3 37 | CA CA CA 1 120.0 527.2 38 | CA CA HA 1 120.0 292.9 39 | CA CA NA 1 120.0 585.8 40 | CA NA CA 1 120.4 585.8 41 | CA NA CT 1 119.8 585.8 42 | NA CA HA 1 120.0 292.9 43 | NA CT HC 1 109.5 292.9 44 | 45 | FB B FB 1 109.5 669.5 46 | 47 | [ dihedraltypes ] 48 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 49 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 50 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 51 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 52 | ; dialkylimidazolium JPCB108:2038(2004) 53 | NA CT CT CT 5 -7.4797 3.1642 -1.2026 0.0000 54 | NA CT CT HC 5 0.0000 0.0000 0.3670 0.0000 55 | ; pyridinium AMBER (cycle) and us 56 | CA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 57 | NA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 58 | HA CA CA NA 5 0.0000 30.3340 0.0000 0.0000 59 | HA CA CA HA 5 0.0000 30.3340 0.0000 0.0000 60 | CA NA CA HA 5 0.0000 12.5520 0.0000 0.0000 61 | CT NA CA HA 5 0.0000 12.5520 0.0000 0.0000 62 | CA NA CA CA 5 0.0000 12.5520 0.0000 0.0000 63 | CT NA CA CA 5 0.0000 12.5520 0.0000 0.0000 64 | HC CT NA CA 5 0.0000 0.0000 0.0000 0.0000 65 | CT CT NA CA 5 0.0000 1.1120 0.0000 0.6900 66 | ; improper pyridinium ring AMBER 67 | CA CA CA HA 5 0.0000 9.2000 0.0000 0.0000 68 | CA CA NA HA 5 0.0000 9.2000 0.0000 0.0000 69 | NA CA CA CT 5 0.0000 8.3700 0.0000 0.0000 70 | -------------------------------------------------------------------------------- /topologies/bpybf4/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "bpy.itp" 3 | #include "bf4.itp" 4 | 5 | [system] 6 | BPY BF4 7 | 8 | 9 | [molecules] 10 | BPY 150 11 | BF4 150 12 | -------------------------------------------------------------------------------- /topologies/bpycl/bpy.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BPY 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CA 1 BPY C1 0 -0.0588 12.011 7 | 2 CA 1 BPY C2 1 0.0000 12.011 8 | 3 NA 1 BPY N3 2 0.1260 14.0067 9 | 4 CA 1 BPY C4 3 0.0000 12.011 10 | 5 CA 1 BPY C5 4 -0.0588 12.011 11 | 6 HA 1 BPY H6 5 0.1260 1.008 12 | 7 HA 1 BPY H7 6 0.1260 1.008 13 | 8 HA 1 BPY H8 7 0.1260 1.008 14 | 9 HA 1 BPY H9 8 0.1260 1.008 15 | 10 CA 1 BPY C10 9 0.0168 12.011 16 | 11 HA 1 BPY H11 10 0.1260 1.008 17 | 12 CT 1 BPY C12 11 -0.1428 12.011 18 | 13 HC 1 BPY H13 12 0.1092 1.008 19 | 14 HC 1 BPY H14 13 0.1092 1.008 20 | 15 CT 1 BPY C15 14 0.0084 12.011 21 | 16 HC 1 BPY H16 15 0.0504 1.008 22 | 17 HC 1 BPY H17 16 0.0504 1.008 23 | 18 CT 1 BPY C18 17 -0.12 12.011 24 | 19 HC 1 BPY H19 18 0.06 1.008 25 | 20 HC 1 BPY H20 19 0.06 1.008 26 | 21 CT 1 BPY C21 20 -0.18 12.011 27 | 22 HC 1 BPY H22 21 0.06 1.008 28 | 23 HC 1 BPY H23 22 0.06 1.008 29 | 24 HC 1 BPY H24 23 0.06 1.008 30 | 31 | [ bonds ] 32 | 1 2 1 33 | 1 6 1 34 | 1 10 1 35 | 2 3 1 36 | 2 7 1 37 | 3 4 1 38 | 3 12 1 39 | 4 5 1 40 | 4 8 1 41 | 5 9 1 42 | 5 10 1 43 | 10 11 1 44 | 12 13 1 45 | 12 14 1 46 | 12 15 1 47 | 15 16 1 48 | 15 17 1 49 | 15 18 1 50 | 18 19 1 51 | 18 20 1 52 | 18 21 1 53 | 21 22 1 54 | 21 23 1 55 | 21 24 1 56 | 57 | [ pairs ] 58 | ; ai aj funct 59 | 1 4 1 60 | 1 9 1 61 | 1 12 1 62 | 2 5 1 63 | 2 8 1 64 | 2 11 1 65 | 2 13 1 66 | 2 14 1 67 | 2 15 1 68 | 3 6 1 69 | 3 9 1 70 | 3 10 1 71 | 3 16 1 72 | 3 17 1 73 | 3 18 1 74 | 4 7 1 75 | 4 11 1 76 | 4 13 1 77 | 4 14 1 78 | 4 15 1 79 | 5 6 1 80 | 5 12 1 81 | 6 7 1 82 | 6 11 1 83 | 7 10 1 84 | 7 12 1 85 | 8 9 1 86 | 8 10 1 87 | 8 12 1 88 | 9 11 1 89 | 12 19 1 90 | 12 20 1 91 | 12 21 1 92 | 13 16 1 93 | 13 17 1 94 | 13 18 1 95 | 14 16 1 96 | 14 17 1 97 | 14 18 1 98 | 15 22 1 99 | 15 23 1 100 | 15 24 1 101 | 16 19 1 102 | 16 20 1 103 | 16 21 1 104 | 17 19 1 105 | 17 20 1 106 | 17 21 1 107 | 19 22 1 108 | 19 23 1 109 | 19 24 1 110 | 20 22 1 111 | 20 23 1 112 | 20 24 1 113 | 114 | [ angles ] 115 | ; ai aj ak funct 116 | 2 1 6 1 117 | 2 1 10 1 118 | 6 1 10 1 119 | 1 2 3 1 120 | 1 2 7 1 121 | 3 2 7 1 122 | 2 3 4 1 123 | 2 3 12 1 124 | 4 3 12 1 125 | 3 4 5 1 126 | 3 4 8 1 127 | 5 4 8 1 128 | 4 5 9 1 129 | 4 5 10 1 130 | 9 5 10 1 131 | 1 10 5 1 132 | 1 10 11 1 133 | 5 10 11 1 134 | 3 12 13 1 135 | 3 12 14 1 136 | 3 12 15 1 137 | 13 12 14 1 138 | 13 12 15 1 139 | 14 12 15 1 140 | 12 15 16 1 141 | 12 15 17 1 142 | 12 15 18 1 143 | 16 15 17 1 144 | 16 15 18 1 145 | 17 15 18 1 146 | 15 18 19 1 147 | 15 18 20 1 148 | 15 18 21 1 149 | 19 18 20 1 150 | 19 18 21 1 151 | 20 18 21 1 152 | 18 21 22 1 153 | 18 21 23 1 154 | 18 21 24 1 155 | 22 21 23 1 156 | 22 21 24 1 157 | 23 21 24 1 158 | 159 | [ dihedrals ] 160 | ;CA-CA-CA-CA 161 | 2 1 10 5 5 162 | 1 10 5 4 5 163 | ;NA-CA-CA-CA 164 | 10 1 2 3 5 165 | 10 5 4 3 5 166 | ;HA-CA-CA-NA 167 | 6 1 2 3 5 168 | 9 5 4 3 5 169 | ;HA-CA-CA-HA 170 | 7 2 1 6 5 171 | 6 1 10 11 5 172 | 9 5 10 11 5 173 | 8 4 5 9 5 174 | ;CA-NA-CA-HA 175 | 2 3 4 8 5 176 | 4 3 2 7 5 177 | ;CT-NA-CA-HA 178 | 12 3 2 7 5 179 | 12 3 4 8 5 180 | ;CA-NA-CA-CA 181 | 2 3 4 5 5 182 | 4 3 2 1 5 183 | ;CT-NA-CA-CA 184 | 12 3 2 1 5 185 | 12 3 4 5 5 186 | ;HC-CT-NA-CA 187 | 13 12 3 2 5 188 | 14 12 3 2 5 189 | 13 12 3 4 5 190 | 14 12 3 4 5 191 | ;CT-CT-NA-CA 192 | 15 12 3 2 5 193 | 15 12 3 4 5 194 | ;NA-CT-CT-CT 195 | 3 12 15 18 5 196 | ;CT-CT-CT-CT 197 | 12 15 18 21 5 198 | ;HC-CT-CT-HC 199 | 13 12 15 16 5 200 | 14 12 15 16 5 201 | 13 12 15 17 5 202 | 14 12 15 18 5 203 | 16 15 18 19 5 204 | 17 15 18 19 5 205 | 16 15 18 20 5 206 | 17 15 18 20 5 207 | 19 18 21 22 5 208 | 19 18 21 23 5 209 | 19 18 21 24 5 210 | 20 18 21 22 5 211 | 20 18 21 23 5 212 | 20 18 21 24 5 213 | ;HC-CT-CT-CT 214 | 13 12 15 18 5 215 | 14 12 15 18 5 216 | 16 15 18 21 5 217 | 17 15 18 21 5 218 | 12 15 18 19 5 219 | 12 15 18 20 5 220 | 15 18 21 22 5 221 | 15 18 21 23 5 222 | 15 18 21 24 5 223 | ;improper dihedrals 224 | ;CA-CA-CA-HA 225 | 5 10 4 9 5 226 | 10 1 5 11 5 227 | 1 2 10 6 5 228 | ;CA-CA-NA-HA 229 | 4 5 3 8 5 230 | 2 3 1 7 5 231 | ;NA-CA-CA-CT 232 | 3 4 2 12 5 233 | -------------------------------------------------------------------------------- /topologies/bpycl/chloride.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | CL 1 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CL 1 CL CL 1 -0.86 35.453 7 | -------------------------------------------------------------------------------- /topologies/bpycl/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ; pyridinium 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NA 7 14.007 0.15 A 0.325 0.71128 10 | CA 6 12.011 0.00 A 0.355 0.29288 11 | HA 1 1.008 0.15 A 0.242 0.12552 12 | 13 | ;Cl 14 | CL 17 35.453 -1.000 A 0.365 0.8300 15 | 16 | ; !!! 17 | [ nonbond_params ] 18 | CL HA 1 0.22 0.3228 19 | CL HC 1 0.22 0.3228 20 | 21 | [ bondtypes ] 22 | NA CT 1 0.1466 282000 23 | HC CT 1 0.1090 -284500 24 | CT CT 1 0.1529 224200 25 | NA HA 1 0.1010 -363200 26 | CA HA 1 0.1080 -307100 27 | CA CA 1 0.1380 392500 28 | CA NA 1 0.1340 404200 29 | 30 | [ angletypes ] 31 | CT CT CT 1 112.7 488.3 32 | CT CT HC 1 110.7 313.8 33 | HC CT HC 1 107.8 276.1 34 | NA CT CT 1 112.7 488.3 35 | CA CA CA 1 120.0 527.2 36 | CA CA HA 1 120.0 292.9 37 | CA CA NA 1 120.0 585.8 38 | CA NA CA 1 120.4 585.8 39 | CA NA CT 1 119.8 585.8 40 | NA CA HA 1 120.0 292.9 41 | NA CT HC 1 109.5 292.9 42 | 43 | [ dihedraltypes ] 44 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 45 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 46 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 47 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 48 | ; dialkylimidazolium JPCB108:2038(2004) 49 | NA CT CT CT 5 -7.4797 3.1642 -1.2026 0.0000 50 | NA CT CT HC 5 0.0000 0.0000 0.3670 0.0000 51 | ; pyridinium AMBER (cycle) and us 52 | CA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 53 | NA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 54 | HA CA CA NA 5 0.0000 30.3340 0.0000 0.0000 55 | HA CA CA HA 5 0.0000 30.3340 0.0000 0.0000 56 | CA NA CA HA 5 0.0000 12.5520 0.0000 0.0000 57 | CT NA CA HA 5 0.0000 12.5520 0.0000 0.0000 58 | CA NA CA CA 5 0.0000 12.5520 0.0000 0.0000 59 | CT NA CA CA 5 0.0000 12.5520 0.0000 0.0000 60 | HC CT NA CA 5 0.0000 0.0000 0.0000 0.0000 61 | CT CT NA CA 5 0.0000 1.1120 0.0000 0.6900 62 | ; improper pyridinium ring AMBER 63 | CA CA CA HA 5 0.0000 9.2000 0.0000 0.0000 64 | CA CA NA HA 5 0.0000 9.2000 0.0000 0.0000 65 | NA CA CA CT 5 0.0000 8.3700 0.0000 0.0000 66 | -------------------------------------------------------------------------------- /topologies/bpycl/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "bpy.itp" 3 | #include "chloride.itp" 4 | 5 | [system] 6 | BPY CL 7 | 8 | 9 | [molecules] 10 | BPY 175 11 | CL 175 12 | -------------------------------------------------------------------------------- /topologies/bpydca/bpy.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BPY 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CA 1 BPY C1 0 -0.0588 12.011 7 | 2 CA 1 BPY C2 1 0.0000 12.011 8 | 3 NA 1 BPY N3 2 0.1260 14.0067 9 | 4 CA 1 BPY C4 3 0.0000 12.011 10 | 5 CA 1 BPY C5 4 -0.0588 12.011 11 | 6 HA 1 BPY H6 5 0.1260 1.008 12 | 7 HA 1 BPY H7 6 0.1260 1.008 13 | 8 HA 1 BPY H8 7 0.1260 1.008 14 | 9 HA 1 BPY H9 8 0.1260 1.008 15 | 10 CA 1 BPY C10 9 0.0168 12.011 16 | 11 HA 1 BPY H11 10 0.1260 1.008 17 | 12 CT 1 BPY C12 11 -0.1428 12.011 18 | 13 HC 1 BPY H13 12 0.1092 1.008 19 | 14 HC 1 BPY H14 13 0.1092 1.008 20 | 15 CT 1 BPY C15 14 0.0084 12.011 21 | 16 HC 1 BPY H16 15 0.0504 1.008 22 | 17 HC 1 BPY H17 16 0.0504 1.008 23 | 18 CT 1 BPY C18 17 -0.12 12.011 24 | 19 HC 1 BPY H19 18 0.06 1.008 25 | 20 HC 1 BPY H20 19 0.06 1.008 26 | 21 CT 1 BPY C21 20 -0.18 12.011 27 | 22 HC 1 BPY H22 21 0.06 1.008 28 | 23 HC 1 BPY H23 22 0.06 1.008 29 | 24 HC 1 BPY H24 23 0.06 1.008 30 | 31 | [ bonds ] 32 | 1 2 1 33 | 1 6 1 34 | 1 10 1 35 | 2 3 1 36 | 2 7 1 37 | 3 4 1 38 | 3 12 1 39 | 4 5 1 40 | 4 8 1 41 | 5 9 1 42 | 5 10 1 43 | 10 11 1 44 | 12 13 1 45 | 12 14 1 46 | 12 15 1 47 | 15 16 1 48 | 15 17 1 49 | 15 18 1 50 | 18 19 1 51 | 18 20 1 52 | 18 21 1 53 | 21 22 1 54 | 21 23 1 55 | 21 24 1 56 | 57 | [ pairs ] 58 | ; ai aj funct 59 | 1 4 1 60 | 1 9 1 61 | 1 12 1 62 | 2 5 1 63 | 2 8 1 64 | 2 11 1 65 | 2 13 1 66 | 2 14 1 67 | 2 15 1 68 | 3 6 1 69 | 3 9 1 70 | 3 10 1 71 | 3 16 1 72 | 3 17 1 73 | 3 18 1 74 | 4 7 1 75 | 4 11 1 76 | 4 13 1 77 | 4 14 1 78 | 4 15 1 79 | 5 6 1 80 | 5 12 1 81 | 6 7 1 82 | 6 11 1 83 | 7 10 1 84 | 7 12 1 85 | 8 9 1 86 | 8 10 1 87 | 8 12 1 88 | 9 11 1 89 | 12 19 1 90 | 12 20 1 91 | 12 21 1 92 | 13 16 1 93 | 13 17 1 94 | 13 18 1 95 | 14 16 1 96 | 14 17 1 97 | 14 18 1 98 | 15 22 1 99 | 15 23 1 100 | 15 24 1 101 | 16 19 1 102 | 16 20 1 103 | 16 21 1 104 | 17 19 1 105 | 17 20 1 106 | 17 21 1 107 | 19 22 1 108 | 19 23 1 109 | 19 24 1 110 | 20 22 1 111 | 20 23 1 112 | 20 24 1 113 | 114 | [ angles ] 115 | ; ai aj ak funct 116 | 2 1 6 1 117 | 2 1 10 1 118 | 6 1 10 1 119 | 1 2 3 1 120 | 1 2 7 1 121 | 3 2 7 1 122 | 2 3 4 1 123 | 2 3 12 1 124 | 4 3 12 1 125 | 3 4 5 1 126 | 3 4 8 1 127 | 5 4 8 1 128 | 4 5 9 1 129 | 4 5 10 1 130 | 9 5 10 1 131 | 1 10 5 1 132 | 1 10 11 1 133 | 5 10 11 1 134 | 3 12 13 1 135 | 3 12 14 1 136 | 3 12 15 1 137 | 13 12 14 1 138 | 13 12 15 1 139 | 14 12 15 1 140 | 12 15 16 1 141 | 12 15 17 1 142 | 12 15 18 1 143 | 16 15 17 1 144 | 16 15 18 1 145 | 17 15 18 1 146 | 15 18 19 1 147 | 15 18 20 1 148 | 15 18 21 1 149 | 19 18 20 1 150 | 19 18 21 1 151 | 20 18 21 1 152 | 18 21 22 1 153 | 18 21 23 1 154 | 18 21 24 1 155 | 22 21 23 1 156 | 22 21 24 1 157 | 23 21 24 1 158 | 159 | [ dihedrals ] 160 | ;CA-CA-CA-CA 161 | 2 1 10 5 5 162 | 1 10 5 4 5 163 | ;NA-CA-CA-CA 164 | 10 1 2 3 5 165 | 10 5 4 3 5 166 | ;HA-CA-CA-NA 167 | 6 1 2 3 5 168 | 9 5 4 3 5 169 | ;HA-CA-CA-HA 170 | 7 2 1 6 5 171 | 6 1 10 11 5 172 | 9 5 10 11 5 173 | 8 4 5 9 5 174 | ;CA-NA-CA-HA 175 | 2 3 4 8 5 176 | 4 3 2 7 5 177 | ;CT-NA-CA-HA 178 | 12 3 2 7 5 179 | 12 3 4 8 5 180 | ;CA-NA-CA-CA 181 | 2 3 4 5 5 182 | 4 3 2 1 5 183 | ;CT-NA-CA-CA 184 | 12 3 2 1 5 185 | 12 3 4 5 5 186 | ;HC-CT-NA-CA 187 | 13 12 3 2 5 188 | 14 12 3 2 5 189 | 13 12 3 4 5 190 | 14 12 3 4 5 191 | ;CT-CT-NA-CA 192 | 15 12 3 2 5 193 | 15 12 3 4 5 194 | ;NA-CT-CT-CT 195 | 3 12 15 18 5 196 | ;CT-CT-CT-CT 197 | 12 15 18 21 5 198 | ;HC-CT-CT-HC 199 | 13 12 15 16 5 200 | 14 12 15 16 5 201 | 13 12 15 17 5 202 | 14 12 15 18 5 203 | 16 15 18 19 5 204 | 17 15 18 19 5 205 | 16 15 18 20 5 206 | 17 15 18 20 5 207 | 19 18 21 22 5 208 | 19 18 21 23 5 209 | 19 18 21 24 5 210 | 20 18 21 22 5 211 | 20 18 21 23 5 212 | 20 18 21 24 5 213 | ;HC-CT-CT-CT 214 | 13 12 15 18 5 215 | 14 12 15 18 5 216 | 16 15 18 21 5 217 | 17 15 18 21 5 218 | 12 15 18 19 5 219 | 12 15 18 20 5 220 | 15 18 21 22 5 221 | 15 18 21 23 5 222 | 15 18 21 24 5 223 | ;improper dihedrals 224 | ;CA-CA-CA-HA 225 | 5 10 4 9 5 226 | 10 1 5 11 5 227 | 1 2 10 6 5 228 | ;CA-CA-NA-HA 229 | 4 5 3 8 5 230 | 2 3 1 7 5 231 | ;NA-CA-CA-CT 232 | 3 4 2 12 5 233 | -------------------------------------------------------------------------------- /topologies/bpydca/dca.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | DCA 3 3 | 4 | [ atoms ] 5 | ;nr type resnr residue atom cgnr charge mass 6 | 1 N3 1 DCA N31 1 -0.68 14.00027 7 | 2 CZ 1 DCA CZ2 2 0.64 12.011 8 | 3 NZ 1 DCA NZ3 3 -0.70 14.00027 9 | 4 CZ 1 DCA CZ4 4 0.64 12.011 10 | 5 NZ 1 DCA NZ5 5 -0.70 14.00027 11 | 12 | [ bonds ] 13 | 1 2 1 14 | 1 4 1 15 | 2 3 1 16 | 4 5 1 17 | 18 | [ angles ] 19 | 2 1 4 1 20 | 1 2 3 1 21 | 1 4 5 1 22 | 23 | [dihedrals] 24 | 4 1 2 3 5 25 | 2 1 4 5 5 26 | -------------------------------------------------------------------------------- /topologies/bpydca/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ; pyridinium 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NA 7 14.007 0.15 A 0.325 0.71128 10 | CA 6 12.011 0.00 A 0.355 0.29288 11 | HA 1 1.008 0.15 A 0.242 0.12552 12 | 13 | ; dicyanamide JPCB110(2006)19586 14 | N3 7 14.00027 -0.76 A 0.325 0.71128 15 | CZ 6 12.011 0.64 A 0.330 0.27614 16 | NZ 7 14.00027 -0.76 A 0.320 0.71128 17 | 18 | [ bondtypes ] 19 | NA CT 1 0.1466 282000 20 | HC CT 1 0.1090 -284500 21 | CT CT 1 0.1529 224200 22 | NA HA 1 0.1010 -363200 23 | CA HA 1 0.1080 -307100 24 | CA CA 1 0.1380 392500 25 | CA NA 1 0.1340 404200 26 | 27 | ; dca- 28 | N3 CZ 1 0.1310 420600 29 | CZ NZ 1 0.1157 774600 30 | 31 | [ angletypes ] 32 | CT CT CT 1 112.7 488.3 33 | CT CT HC 1 110.7 313.8 34 | HC CT HC 1 107.8 276.1 35 | NA CT CT 1 112.7 488.3 36 | CA CA CA 1 120.0 527.2 37 | CA CA HA 1 120.0 292.9 38 | CA CA NA 1 120.0 585.8 39 | CA NA CA 1 120.4 585.8 40 | CA NA CT 1 119.8 585.8 41 | NA CA HA 1 120.0 292.9 42 | NA CT HC 1 109.5 292.9 43 | 44 | CZ N3 CZ 1 118.5 362.0 45 | N3 CZ NZ 1 175.2 425.0 46 | 47 | [ dihedraltypes ] 48 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 49 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 50 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 51 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 52 | ; dialkylimidazolium JPCB108:2038(2004) 53 | NA CT CT CT 5 -7.4797 3.1642 -1.2026 0.0000 54 | NA CT CT HC 5 0.0000 0.0000 0.3670 0.0000 55 | ; pyridinium AMBER (cycle) and us 56 | CA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 57 | NA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 58 | HA CA CA NA 5 0.0000 30.3340 0.0000 0.0000 59 | HA CA CA HA 5 0.0000 30.3340 0.0000 0.0000 60 | CA NA CA HA 5 0.0000 12.5520 0.0000 0.0000 61 | CT NA CA HA 5 0.0000 12.5520 0.0000 0.0000 62 | CA NA CA CA 5 0.0000 12.5520 0.0000 0.0000 63 | CT NA CA CA 5 0.0000 12.5520 0.0000 0.0000 64 | HC CT NA CA 5 0.0000 0.0000 0.0000 0.0000 65 | CT CT NA CA 5 0.0000 1.1120 0.0000 0.6900 66 | ; improper pyridinium ring AMBER 67 | CA CA CA HA 5 0.0000 9.2000 0.0000 0.0000 68 | CA CA NA HA 5 0.0000 9.2000 0.0000 0.0000 69 | NA CA CA CT 5 0.0000 8.3700 0.0000 0.0000 70 | ; dca- CL&P 71 | NZ CZ N3 CZ 5 4.0800 0.0000 0.0000 0.0000 72 | -------------------------------------------------------------------------------- /topologies/bpydca/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "bpy.itp" 3 | #include "dca.itp" 4 | 5 | [system] 6 | BPY DCA 7 | 8 | 9 | [molecules] 10 | BPY 150 11 | DCA 150 12 | -------------------------------------------------------------------------------- /topologies/bpypf6/bpy.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BPY 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CA 1 BPY C1 0 -0.0588 12.011 7 | 2 CA 1 BPY C2 1 0.0000 12.011 8 | 3 NA 1 BPY N3 2 0.1260 14.0067 9 | 4 CA 1 BPY C4 3 0.0000 12.011 10 | 5 CA 1 BPY C5 4 -0.0588 12.011 11 | 6 HA 1 BPY H6 5 0.1260 1.008 12 | 7 HA 1 BPY H7 6 0.1260 1.008 13 | 8 HA 1 BPY H8 7 0.1260 1.008 14 | 9 HA 1 BPY H9 8 0.1260 1.008 15 | 10 CA 1 BPY C10 9 0.0168 12.011 16 | 11 HA 1 BPY H11 10 0.1260 1.008 17 | 12 CT 1 BPY C12 11 -0.1428 12.011 18 | 13 HC 1 BPY H13 12 0.1092 1.008 19 | 14 HC 1 BPY H14 13 0.1092 1.008 20 | 15 CT 1 BPY C15 14 0.0084 12.011 21 | 16 HC 1 BPY H16 15 0.0504 1.008 22 | 17 HC 1 BPY H17 16 0.0504 1.008 23 | 18 CT 1 BPY C18 17 -0.12 12.011 24 | 19 HC 1 BPY H19 18 0.06 1.008 25 | 20 HC 1 BPY H20 19 0.06 1.008 26 | 21 CT 1 BPY C21 20 -0.18 12.011 27 | 22 HC 1 BPY H22 21 0.06 1.008 28 | 23 HC 1 BPY H23 22 0.06 1.008 29 | 24 HC 1 BPY H24 23 0.06 1.008 30 | 31 | [ bonds ] 32 | 1 2 1 33 | 1 6 1 34 | 1 10 1 35 | 2 3 1 36 | 2 7 1 37 | 3 4 1 38 | 3 12 1 39 | 4 5 1 40 | 4 8 1 41 | 5 9 1 42 | 5 10 1 43 | 10 11 1 44 | 12 13 1 45 | 12 14 1 46 | 12 15 1 47 | 15 16 1 48 | 15 17 1 49 | 15 18 1 50 | 18 19 1 51 | 18 20 1 52 | 18 21 1 53 | 21 22 1 54 | 21 23 1 55 | 21 24 1 56 | 57 | [ pairs ] 58 | ; ai aj funct 59 | 1 4 1 60 | 1 9 1 61 | 1 12 1 62 | 2 5 1 63 | 2 8 1 64 | 2 11 1 65 | 2 13 1 66 | 2 14 1 67 | 2 15 1 68 | 3 6 1 69 | 3 9 1 70 | 3 10 1 71 | 3 16 1 72 | 3 17 1 73 | 3 18 1 74 | 4 7 1 75 | 4 11 1 76 | 4 13 1 77 | 4 14 1 78 | 4 15 1 79 | 5 6 1 80 | 5 12 1 81 | 6 7 1 82 | 6 11 1 83 | 7 10 1 84 | 7 12 1 85 | 8 9 1 86 | 8 10 1 87 | 8 12 1 88 | 9 11 1 89 | 12 19 1 90 | 12 20 1 91 | 12 21 1 92 | 13 16 1 93 | 13 17 1 94 | 13 18 1 95 | 14 16 1 96 | 14 17 1 97 | 14 18 1 98 | 15 22 1 99 | 15 23 1 100 | 15 24 1 101 | 16 19 1 102 | 16 20 1 103 | 16 21 1 104 | 17 19 1 105 | 17 20 1 106 | 17 21 1 107 | 19 22 1 108 | 19 23 1 109 | 19 24 1 110 | 20 22 1 111 | 20 23 1 112 | 20 24 1 113 | 114 | [ angles ] 115 | ; ai aj ak funct 116 | 2 1 6 1 117 | 2 1 10 1 118 | 6 1 10 1 119 | 1 2 3 1 120 | 1 2 7 1 121 | 3 2 7 1 122 | 2 3 4 1 123 | 2 3 12 1 124 | 4 3 12 1 125 | 3 4 5 1 126 | 3 4 8 1 127 | 5 4 8 1 128 | 4 5 9 1 129 | 4 5 10 1 130 | 9 5 10 1 131 | 1 10 5 1 132 | 1 10 11 1 133 | 5 10 11 1 134 | 3 12 13 1 135 | 3 12 14 1 136 | 3 12 15 1 137 | 13 12 14 1 138 | 13 12 15 1 139 | 14 12 15 1 140 | 12 15 16 1 141 | 12 15 17 1 142 | 12 15 18 1 143 | 16 15 17 1 144 | 16 15 18 1 145 | 17 15 18 1 146 | 15 18 19 1 147 | 15 18 20 1 148 | 15 18 21 1 149 | 19 18 20 1 150 | 19 18 21 1 151 | 20 18 21 1 152 | 18 21 22 1 153 | 18 21 23 1 154 | 18 21 24 1 155 | 22 21 23 1 156 | 22 21 24 1 157 | 23 21 24 1 158 | 159 | [ dihedrals ] 160 | ;CA-CA-CA-CA 161 | 2 1 10 5 5 162 | 1 10 5 4 5 163 | ;NA-CA-CA-CA 164 | 10 1 2 3 5 165 | 10 5 4 3 5 166 | ;HA-CA-CA-NA 167 | 6 1 2 3 5 168 | 9 5 4 3 5 169 | ;HA-CA-CA-HA 170 | 7 2 1 6 5 171 | 6 1 10 11 5 172 | 9 5 10 11 5 173 | 8 4 5 9 5 174 | ;CA-NA-CA-HA 175 | 2 3 4 8 5 176 | 4 3 2 7 5 177 | ;CT-NA-CA-HA 178 | 12 3 2 7 5 179 | 12 3 4 8 5 180 | ;CA-NA-CA-CA 181 | 2 3 4 5 5 182 | 4 3 2 1 5 183 | ;CT-NA-CA-CA 184 | 12 3 2 1 5 185 | 12 3 4 5 5 186 | ;HC-CT-NA-CA 187 | 13 12 3 2 5 188 | 14 12 3 2 5 189 | 13 12 3 4 5 190 | 14 12 3 4 5 191 | ;CT-CT-NA-CA 192 | 15 12 3 2 5 193 | 15 12 3 4 5 194 | ;NA-CT-CT-CT 195 | 3 12 15 18 5 196 | ;CT-CT-CT-CT 197 | 12 15 18 21 5 198 | ;HC-CT-CT-HC 199 | 13 12 15 16 5 200 | 14 12 15 16 5 201 | 13 12 15 17 5 202 | 14 12 15 18 5 203 | 16 15 18 19 5 204 | 17 15 18 19 5 205 | 16 15 18 20 5 206 | 17 15 18 20 5 207 | 19 18 21 22 5 208 | 19 18 21 23 5 209 | 19 18 21 24 5 210 | 20 18 21 22 5 211 | 20 18 21 23 5 212 | 20 18 21 24 5 213 | ;HC-CT-CT-CT 214 | 13 12 15 18 5 215 | 14 12 15 18 5 216 | 16 15 18 21 5 217 | 17 15 18 21 5 218 | 12 15 18 19 5 219 | 12 15 18 20 5 220 | 15 18 21 22 5 221 | 15 18 21 23 5 222 | 15 18 21 24 5 223 | ;improper dihedrals 224 | ;CA-CA-CA-HA 225 | 5 10 4 9 5 226 | 10 1 5 11 5 227 | 1 2 10 6 5 228 | ;CA-CA-NA-HA 229 | 4 5 3 8 5 230 | 2 3 1 7 5 231 | ;NA-CA-CA-CT 232 | 3 4 2 12 5 233 | -------------------------------------------------------------------------------- /topologies/bpypf6/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ; pyridinium 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NA 7 14.007 0.15 A 0.325 0.71128 10 | CA 6 12.011 0.00 A 0.355 0.29288 11 | HA 1 1.008 0.15 A 0.242 0.12552 12 | 13 | ;hexafluorophosphate JCSPerkin2(1999)2365 14 | P 15 30.974 1.34 A 0.374 0.83680 15 | FP 9 18.998 -0.39 A 0.312 0.25520 16 | 17 | ; !!! 18 | [ nonbond_params ] 19 | FP HC 1 0.19 0.18 20 | 21 | [ bondtypes ] 22 | NA CT 1 0.1466 282000 23 | HC CT 1 0.1090 -284500 24 | CT CT 1 0.1529 224200 25 | NA HA 1 0.1010 -363200 26 | CA HA 1 0.1080 -307100 27 | CA CA 1 0.1380 392500 28 | CA NA 1 0.1340 404200 29 | 30 | ;hexafluorophosphate JCSPerkin2(1999)2365 31 | P FP 1 0.1606 310000 32 | 33 | [ angletypes ] 34 | CT CT CT 1 112.7 488.3 35 | CT CT HC 1 110.7 313.8 36 | HC CT HC 1 107.8 276.1 37 | NA CT CT 1 112.7 488.3 38 | CA CA CA 1 120.0 527.2 39 | CA CA HA 1 120.0 292.9 40 | CA CA NA 1 120.0 585.8 41 | CA NA CA 1 120.4 585.8 42 | CA NA CT 1 119.8 585.8 43 | NA CA HA 1 120.0 292.9 44 | NA CT HC 1 109.5 292.9 45 | ;hexafluorophosphate JCSPerkin2(1999)2365 46 | FP P FP 1 90.0 1165.0 47 | 48 | [ dihedraltypes ] 49 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 50 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 51 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 52 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 53 | ; dialkylimidazolium JPCB108:2038(2004) 54 | NA CT CT CT 5 -7.4797 3.1642 -1.2026 0.0000 55 | NA CT CT HC 5 0.0000 0.0000 0.3670 0.0000 56 | ; pyridinium AMBER (cycle) and us 57 | CA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 58 | NA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 59 | HA CA CA NA 5 0.0000 30.3340 0.0000 0.0000 60 | HA CA CA HA 5 0.0000 30.3340 0.0000 0.0000 61 | CA NA CA HA 5 0.0000 12.5520 0.0000 0.0000 62 | CT NA CA HA 5 0.0000 12.5520 0.0000 0.0000 63 | CA NA CA CA 5 0.0000 12.5520 0.0000 0.0000 64 | CT NA CA CA 5 0.0000 12.5520 0.0000 0.0000 65 | HC CT NA CA 5 0.0000 0.0000 0.0000 0.0000 66 | CT CT NA CA 5 0.0000 1.1120 0.0000 0.6900 67 | ; improper pyridinium ring AMBER 68 | CA CA CA HA 5 0.0000 9.2000 0.0000 0.0000 69 | CA CA NA HA 5 0.0000 9.2000 0.0000 0.0000 70 | NA CA CA CT 5 0.0000 8.3700 0.0000 0.0000 71 | -------------------------------------------------------------------------------- /topologies/bpypf6/pf6.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | PF6 2 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 P 1 PF6 P1 1 1.13 30.974 7 | 2 FP 1 PF6 F2 2 -0.33 18.998 8 | 3 FP 1 PF6 F3 3 -0.33 18.998 9 | 4 FP 1 PF6 F4 4 -0.33 18.998 10 | 5 FP 1 PF6 F5 5 -0.33 18.998 11 | 6 FP 1 PF6 F6 6 -0.33 18.998 12 | 7 FP 1 PF6 F7 7 -0.33 18.998 13 | 14 | [ bonds ] 15 | 1 2 1 16 | 1 3 1 17 | 1 4 1 18 | 1 5 1 19 | 1 6 1 20 | 1 7 1 21 | 22 | [ angles ] 23 | 2 1 3 1 24 | 2 1 4 1 25 | 2 1 6 1 26 | 2 1 7 1 27 | 28 | 3 1 4 1 29 | 3 1 5 1 30 | 3 1 7 1 31 | 32 | 4 1 5 1 33 | 4 1 6 1 34 | 35 | 5 1 6 1 36 | 5 1 7 1 37 | 38 | 6 1 7 1 39 | 40 | 41 | 2 1 5 1 180. 1165. 42 | 3 1 6 1 180. 1165. 43 | 4 1 7 1 180. 1165. 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /topologies/bpypf6/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "bpy.itp" 3 | #include "pf6.itp" 4 | 5 | [system] 6 | BPY PF6 7 | 8 | 9 | [molecules] 10 | BPY 125 11 | PF6 125 12 | -------------------------------------------------------------------------------- /topologies/bpytf/bpy.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BPY 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CA 1 BPY C1 0 -0.0588 12.011 7 | 2 CA 1 BPY C2 1 0.0000 12.011 8 | 3 NA 1 BPY N3 2 0.1260 14.0067 9 | 4 CA 1 BPY C4 3 0.0000 12.011 10 | 5 CA 1 BPY C5 4 -0.0588 12.011 11 | 6 HA 1 BPY H6 5 0.1260 1.008 12 | 7 HA 1 BPY H7 6 0.1260 1.008 13 | 8 HA 1 BPY H8 7 0.1260 1.008 14 | 9 HA 1 BPY H9 8 0.1260 1.008 15 | 10 CA 1 BPY C10 9 0.0168 12.011 16 | 11 HA 1 BPY H11 10 0.1260 1.008 17 | 12 CT 1 BPY C12 11 -0.1428 12.011 18 | 13 HC 1 BPY H13 12 0.1092 1.008 19 | 14 HC 1 BPY H14 13 0.1092 1.008 20 | 15 CT 1 BPY C15 14 0.0084 12.011 21 | 16 HC 1 BPY H16 15 0.0504 1.008 22 | 17 HC 1 BPY H17 16 0.0504 1.008 23 | 18 CT 1 BPY C18 17 -0.12 12.011 24 | 19 HC 1 BPY H19 18 0.06 1.008 25 | 20 HC 1 BPY H20 19 0.06 1.008 26 | 21 CT 1 BPY C21 20 -0.18 12.011 27 | 22 HC 1 BPY H22 21 0.06 1.008 28 | 23 HC 1 BPY H23 22 0.06 1.008 29 | 24 HC 1 BPY H24 23 0.06 1.008 30 | 31 | [ bonds ] 32 | 1 2 1 33 | 1 6 1 34 | 1 10 1 35 | 2 3 1 36 | 2 7 1 37 | 3 4 1 38 | 3 12 1 39 | 4 5 1 40 | 4 8 1 41 | 5 9 1 42 | 5 10 1 43 | 10 11 1 44 | 12 13 1 45 | 12 14 1 46 | 12 15 1 47 | 15 16 1 48 | 15 17 1 49 | 15 18 1 50 | 18 19 1 51 | 18 20 1 52 | 18 21 1 53 | 21 22 1 54 | 21 23 1 55 | 21 24 1 56 | 57 | [ pairs ] 58 | ; ai aj funct 59 | 1 4 1 60 | 1 9 1 61 | 1 12 1 62 | 2 5 1 63 | 2 8 1 64 | 2 11 1 65 | 2 13 1 66 | 2 14 1 67 | 2 15 1 68 | 3 6 1 69 | 3 9 1 70 | 3 10 1 71 | 3 16 1 72 | 3 17 1 73 | 3 18 1 74 | 4 7 1 75 | 4 11 1 76 | 4 13 1 77 | 4 14 1 78 | 4 15 1 79 | 5 6 1 80 | 5 12 1 81 | 6 7 1 82 | 6 11 1 83 | 7 10 1 84 | 7 12 1 85 | 8 9 1 86 | 8 10 1 87 | 8 12 1 88 | 9 11 1 89 | 12 19 1 90 | 12 20 1 91 | 12 21 1 92 | 13 16 1 93 | 13 17 1 94 | 13 18 1 95 | 14 16 1 96 | 14 17 1 97 | 14 18 1 98 | 15 22 1 99 | 15 23 1 100 | 15 24 1 101 | 16 19 1 102 | 16 20 1 103 | 16 21 1 104 | 17 19 1 105 | 17 20 1 106 | 17 21 1 107 | 19 22 1 108 | 19 23 1 109 | 19 24 1 110 | 20 22 1 111 | 20 23 1 112 | 20 24 1 113 | 114 | [ angles ] 115 | ; ai aj ak funct 116 | 2 1 6 1 117 | 2 1 10 1 118 | 6 1 10 1 119 | 1 2 3 1 120 | 1 2 7 1 121 | 3 2 7 1 122 | 2 3 4 1 123 | 2 3 12 1 124 | 4 3 12 1 125 | 3 4 5 1 126 | 3 4 8 1 127 | 5 4 8 1 128 | 4 5 9 1 129 | 4 5 10 1 130 | 9 5 10 1 131 | 1 10 5 1 132 | 1 10 11 1 133 | 5 10 11 1 134 | 3 12 13 1 135 | 3 12 14 1 136 | 3 12 15 1 137 | 13 12 14 1 138 | 13 12 15 1 139 | 14 12 15 1 140 | 12 15 16 1 141 | 12 15 17 1 142 | 12 15 18 1 143 | 16 15 17 1 144 | 16 15 18 1 145 | 17 15 18 1 146 | 15 18 19 1 147 | 15 18 20 1 148 | 15 18 21 1 149 | 19 18 20 1 150 | 19 18 21 1 151 | 20 18 21 1 152 | 18 21 22 1 153 | 18 21 23 1 154 | 18 21 24 1 155 | 22 21 23 1 156 | 22 21 24 1 157 | 23 21 24 1 158 | 159 | [ dihedrals ] 160 | ;CA-CA-CA-CA 161 | 2 1 10 5 5 162 | 1 10 5 4 5 163 | ;NA-CA-CA-CA 164 | 10 1 2 3 5 165 | 10 5 4 3 5 166 | ;HA-CA-CA-NA 167 | 6 1 2 3 5 168 | 9 5 4 3 5 169 | ;HA-CA-CA-HA 170 | 7 2 1 6 5 171 | 6 1 10 11 5 172 | 9 5 10 11 5 173 | 8 4 5 9 5 174 | ;CA-NA-CA-HA 175 | 2 3 4 8 5 176 | 4 3 2 7 5 177 | ;CT-NA-CA-HA 178 | 12 3 2 7 5 179 | 12 3 4 8 5 180 | ;CA-NA-CA-CA 181 | 2 3 4 5 5 182 | 4 3 2 1 5 183 | ;CT-NA-CA-CA 184 | 12 3 2 1 5 185 | 12 3 4 5 5 186 | ;HC-CT-NA-CA 187 | 13 12 3 2 5 188 | 14 12 3 2 5 189 | 13 12 3 4 5 190 | 14 12 3 4 5 191 | ;CT-CT-NA-CA 192 | 15 12 3 2 5 193 | 15 12 3 4 5 194 | ;NA-CT-CT-CT 195 | 3 12 15 18 5 196 | ;CT-CT-CT-CT 197 | 12 15 18 21 5 198 | ;HC-CT-CT-HC 199 | 13 12 15 16 5 200 | 14 12 15 16 5 201 | 13 12 15 17 5 202 | 14 12 15 18 5 203 | 16 15 18 19 5 204 | 17 15 18 19 5 205 | 16 15 18 20 5 206 | 17 15 18 20 5 207 | 19 18 21 22 5 208 | 19 18 21 23 5 209 | 19 18 21 24 5 210 | 20 18 21 22 5 211 | 20 18 21 23 5 212 | 20 18 21 24 5 213 | ;HC-CT-CT-CT 214 | 13 12 15 18 5 215 | 14 12 15 18 5 216 | 16 15 18 21 5 217 | 17 15 18 21 5 218 | 12 15 18 19 5 219 | 12 15 18 20 5 220 | 15 18 21 22 5 221 | 15 18 21 23 5 222 | 15 18 21 24 5 223 | ;improper dihedrals 224 | ;CA-CA-CA-HA 225 | 5 10 4 9 5 226 | 10 1 5 11 5 227 | 1 2 10 6 5 228 | ;CA-CA-NA-HA 229 | 4 5 3 8 5 230 | 2 3 1 7 5 231 | ;NA-CA-CA-CT 232 | 3 4 2 12 5 233 | -------------------------------------------------------------------------------- /topologies/bpytf/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ; pyridinium 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NA 7 14.007 0.15 A 0.325 0.71128 10 | CA 6 12.011 0.00 A 0.355 0.29288 11 | HA 1 1.008 0.15 A 0.242 0.12552 12 | 13 | ;TF 14 | SB 16 32.064 1.02 A 0.355 1.04600 15 | OB 8 15.9994 -0.63 A 0.296 0.87864 16 | FB 9 18.9984 -0.16 A 0.295 0.22175 17 | CB 6 12.011 0.35 A 0.350 0.27614 18 | 19 | [ bondtypes ] 20 | NA CT 1 0.1466 282000 21 | HC CT 1 0.1090 -284500 22 | CT CT 1 0.1529 224200 23 | NA HA 1 0.1010 -363200 24 | CA HA 1 0.1080 -307100 25 | CA CA 1 0.1380 392500 26 | CA NA 1 0.1340 404200 27 | 28 | ;TF 29 | CB FB 1 0.1323 369800 30 | CB SB 1 0.1818 195000 31 | SB OB 1 0.1437 533100 32 | 33 | [ angletypes ] 34 | CT CT CT 1 112.7 488.3 35 | CT CT HC 1 110.7 313.8 36 | HC CT HC 1 107.8 276.1 37 | NA CT CT 1 112.7 488.3 38 | CA CA CA 1 120.0 527.2 39 | CA CA HA 1 120.0 292.9 40 | CA CA NA 1 120.0 585.8 41 | CA NA CA 1 120.4 585.8 42 | CA NA CT 1 119.8 585.8 43 | NA CA HA 1 120.0 292.9 44 | NA CT HC 1 109.5 292.9 45 | 46 | ;TF 47 | FB CB FB 1 107.1 781.0 48 | FB CB SB 1 111.7 694.0 49 | OB SB OB 1 118.5 969.0 50 | CB SB OB 1 102.6 870.0 51 | 52 | [ dihedraltypes ] 53 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 54 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 55 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 56 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 57 | ; dialkylimidazolium JPCB108:2038(2004) 58 | NA CT CT CT 5 -7.4797 3.1642 -1.2026 0.0000 59 | NA CT CT HC 5 0.0000 0.0000 0.3670 0.0000 60 | ; pyridinium AMBER (cycle) and us 61 | CA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 62 | NA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 63 | HA CA CA NA 5 0.0000 30.3340 0.0000 0.0000 64 | HA CA CA HA 5 0.0000 30.3340 0.0000 0.0000 65 | CA NA CA HA 5 0.0000 12.5520 0.0000 0.0000 66 | CT NA CA HA 5 0.0000 12.5520 0.0000 0.0000 67 | CA NA CA CA 5 0.0000 12.5520 0.0000 0.0000 68 | CT NA CA CA 5 0.0000 12.5520 0.0000 0.0000 69 | HC CT NA CA 5 0.0000 0.0000 0.0000 0.0000 70 | CT CT NA CA 5 0.0000 1.1120 0.0000 0.6900 71 | ; improper pyridinium ring AMBER 72 | CA CA CA HA 5 0.0000 9.2000 0.0000 0.0000 73 | CA CA NA HA 5 0.0000 9.2000 0.0000 0.0000 74 | NA CA CA CT 5 0.0000 8.3700 0.0000 0.0000 75 | ;triflate JPCB108(2004)16893 76 | OB SB CB FB 5 0.0000 0.0000 1.4510 0.0000 77 | -------------------------------------------------------------------------------- /topologies/bpytf/tf.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | TF 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CB 1 TF C1 1 0.34 12.011 7 | 2 FB 1 TF F2 2 -0.15 18.998 8 | 3 FB 1 TF F3 3 -0.15 18.998 9 | 4 FB 1 TF F4 4 -0.15 18.998 10 | 5 SB 1 TF S5 5 1.01 32.066 11 | 6 OB 1 TF O6 6 -0.56 15.999 12 | 7 OB 1 TF O7 7 -0.56 15.999 13 | 8 OB 1 TF O8 8 -0.56 15.999 14 | 15 | [ bonds ] 16 | 1 2 1 17 | 1 3 1 18 | 1 4 1 19 | 1 5 1 20 | 5 6 1 21 | 5 7 1 22 | 5 8 1 23 | 24 | [ angles ] 25 | 2 1 3 1 26 | 2 1 4 1 27 | 3 1 4 1 28 | 2 1 5 1 29 | 3 1 5 1 30 | 4 1 5 1 31 | 6 5 7 1 32 | 6 5 8 1 33 | 7 5 8 1 34 | 1 5 6 1 35 | 1 5 7 1 36 | 1 5 8 1 37 | 38 | [ dihedrals ] 39 | 6 5 1 2 5 40 | 6 5 1 3 5 41 | 6 5 1 4 5 42 | 7 5 1 2 5 43 | 7 5 1 3 5 44 | 7 5 1 4 5 45 | 8 5 1 2 5 46 | 8 5 1 3 5 47 | 8 5 1 4 5 48 | -------------------------------------------------------------------------------- /topologies/bpytf/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "bpy.itp" 3 | #include "tf.itp" 4 | 5 | [system] 6 | BPY TF 7 | 8 | 9 | [molecules] 10 | BPY 125 11 | TF 125 12 | -------------------------------------------------------------------------------- /topologies/bpytfsi/bpy.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BPY 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CA 1 BPY C1 0 -0.0588 12.011 7 | 2 CA 1 BPY C2 1 0.0000 12.011 8 | 3 NA 1 BPY N3 2 0.1260 14.0067 9 | 4 CA 1 BPY C4 3 0.0000 12.011 10 | 5 CA 1 BPY C5 4 -0.0588 12.011 11 | 6 HA 1 BPY H6 5 0.1260 1.008 12 | 7 HA 1 BPY H7 6 0.1260 1.008 13 | 8 HA 1 BPY H8 7 0.1260 1.008 14 | 9 HA 1 BPY H9 8 0.1260 1.008 15 | 10 CA 1 BPY C10 9 0.0168 12.011 16 | 11 HA 1 BPY H11 10 0.1260 1.008 17 | 12 CT 1 BPY C12 11 -0.1428 12.011 18 | 13 HC 1 BPY H13 12 0.1092 1.008 19 | 14 HC 1 BPY H14 13 0.1092 1.008 20 | 15 CT 1 BPY C15 14 0.0084 12.011 21 | 16 HC 1 BPY H16 15 0.0504 1.008 22 | 17 HC 1 BPY H17 16 0.0504 1.008 23 | 18 CT 1 BPY C18 17 -0.12 12.011 24 | 19 HC 1 BPY H19 18 0.06 1.008 25 | 20 HC 1 BPY H20 19 0.06 1.008 26 | 21 CT 1 BPY C21 20 -0.18 12.011 27 | 22 HC 1 BPY H22 21 0.06 1.008 28 | 23 HC 1 BPY H23 22 0.06 1.008 29 | 24 HC 1 BPY H24 23 0.06 1.008 30 | 31 | [ bonds ] 32 | 1 2 1 33 | 1 6 1 34 | 1 10 1 35 | 2 3 1 36 | 2 7 1 37 | 3 4 1 38 | 3 12 1 39 | 4 5 1 40 | 4 8 1 41 | 5 9 1 42 | 5 10 1 43 | 10 11 1 44 | 12 13 1 45 | 12 14 1 46 | 12 15 1 47 | 15 16 1 48 | 15 17 1 49 | 15 18 1 50 | 18 19 1 51 | 18 20 1 52 | 18 21 1 53 | 21 22 1 54 | 21 23 1 55 | 21 24 1 56 | 57 | [ pairs ] 58 | ; ai aj funct 59 | 1 4 1 60 | 1 9 1 61 | 1 12 1 62 | 2 5 1 63 | 2 8 1 64 | 2 11 1 65 | 2 13 1 66 | 2 14 1 67 | 2 15 1 68 | 3 6 1 69 | 3 9 1 70 | 3 10 1 71 | 3 16 1 72 | 3 17 1 73 | 3 18 1 74 | 4 7 1 75 | 4 11 1 76 | 4 13 1 77 | 4 14 1 78 | 4 15 1 79 | 5 6 1 80 | 5 12 1 81 | 6 7 1 82 | 6 11 1 83 | 7 10 1 84 | 7 12 1 85 | 8 9 1 86 | 8 10 1 87 | 8 12 1 88 | 9 11 1 89 | 12 19 1 90 | 12 20 1 91 | 12 21 1 92 | 13 16 1 93 | 13 17 1 94 | 13 18 1 95 | 14 16 1 96 | 14 17 1 97 | 14 18 1 98 | 15 22 1 99 | 15 23 1 100 | 15 24 1 101 | 16 19 1 102 | 16 20 1 103 | 16 21 1 104 | 17 19 1 105 | 17 20 1 106 | 17 21 1 107 | 19 22 1 108 | 19 23 1 109 | 19 24 1 110 | 20 22 1 111 | 20 23 1 112 | 20 24 1 113 | 114 | [ angles ] 115 | ; ai aj ak funct 116 | 2 1 6 1 117 | 2 1 10 1 118 | 6 1 10 1 119 | 1 2 3 1 120 | 1 2 7 1 121 | 3 2 7 1 122 | 2 3 4 1 123 | 2 3 12 1 124 | 4 3 12 1 125 | 3 4 5 1 126 | 3 4 8 1 127 | 5 4 8 1 128 | 4 5 9 1 129 | 4 5 10 1 130 | 9 5 10 1 131 | 1 10 5 1 132 | 1 10 11 1 133 | 5 10 11 1 134 | 3 12 13 1 135 | 3 12 14 1 136 | 3 12 15 1 137 | 13 12 14 1 138 | 13 12 15 1 139 | 14 12 15 1 140 | 12 15 16 1 141 | 12 15 17 1 142 | 12 15 18 1 143 | 16 15 17 1 144 | 16 15 18 1 145 | 17 15 18 1 146 | 15 18 19 1 147 | 15 18 20 1 148 | 15 18 21 1 149 | 19 18 20 1 150 | 19 18 21 1 151 | 20 18 21 1 152 | 18 21 22 1 153 | 18 21 23 1 154 | 18 21 24 1 155 | 22 21 23 1 156 | 22 21 24 1 157 | 23 21 24 1 158 | 159 | [ dihedrals ] 160 | ;CA-CA-CA-CA 161 | 2 1 10 5 5 162 | 1 10 5 4 5 163 | ;NA-CA-CA-CA 164 | 10 1 2 3 5 165 | 10 5 4 3 5 166 | ;HA-CA-CA-NA 167 | 6 1 2 3 5 168 | 9 5 4 3 5 169 | ;HA-CA-CA-HA 170 | 7 2 1 6 5 171 | 6 1 10 11 5 172 | 9 5 10 11 5 173 | 8 4 5 9 5 174 | ;CA-NA-CA-HA 175 | 2 3 4 8 5 176 | 4 3 2 7 5 177 | ;CT-NA-CA-HA 178 | 12 3 2 7 5 179 | 12 3 4 8 5 180 | ;CA-NA-CA-CA 181 | 2 3 4 5 5 182 | 4 3 2 1 5 183 | ;CT-NA-CA-CA 184 | 12 3 2 1 5 185 | 12 3 4 5 5 186 | ;HC-CT-NA-CA 187 | 13 12 3 2 5 188 | 14 12 3 2 5 189 | 13 12 3 4 5 190 | 14 12 3 4 5 191 | ;CT-CT-NA-CA 192 | 15 12 3 2 5 193 | 15 12 3 4 5 194 | ;NA-CT-CT-CT 195 | 3 12 15 18 5 196 | ;CT-CT-CT-CT 197 | 12 15 18 21 5 198 | ;HC-CT-CT-HC 199 | 13 12 15 16 5 200 | 14 12 15 16 5 201 | 13 12 15 17 5 202 | 14 12 15 18 5 203 | 16 15 18 19 5 204 | 17 15 18 19 5 205 | 16 15 18 20 5 206 | 17 15 18 20 5 207 | 19 18 21 22 5 208 | 19 18 21 23 5 209 | 19 18 21 24 5 210 | 20 18 21 22 5 211 | 20 18 21 23 5 212 | 20 18 21 24 5 213 | ;HC-CT-CT-CT 214 | 13 12 15 18 5 215 | 14 12 15 18 5 216 | 16 15 18 21 5 217 | 17 15 18 21 5 218 | 12 15 18 19 5 219 | 12 15 18 20 5 220 | 15 18 21 22 5 221 | 15 18 21 23 5 222 | 15 18 21 24 5 223 | ;improper dihedrals 224 | ;CA-CA-CA-HA 225 | 5 10 4 9 5 226 | 10 1 5 11 5 227 | 1 2 10 6 5 228 | ;CA-CA-NA-HA 229 | 4 5 3 8 5 230 | 2 3 1 7 5 231 | ;NA-CA-CA-CT 232 | 3 4 2 12 5 233 | -------------------------------------------------------------------------------- /topologies/bpytfsi/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ; pyridinium 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NA 7 14.007 0.15 A 0.325 0.71128 10 | CA 6 12.011 0.00 A 0.355 0.29288 11 | HA 1 1.008 0.15 A 0.242 0.12552 12 | 13 | ; TFSI 14 | SO 16 32.064 1.02 A 0.355 1.04600 15 | OS 8 15.9994 -0.53 A 0.296 0.87864 16 | FC 9 18.9984 -0.16 A 0.295 0.22175 17 | CF 6 12.011 0.35 A 0.350 0.27614 18 | NI 7 14.0027 -0.66 A 0.325 0.71128 19 | 20 | ; !!! 21 | [ nonbond_params ] 22 | ;OS HC 1 0.207 0.33 23 | 24 | [ bondtypes ] 25 | NA CT 1 0.1466 282000 26 | HC CT 1 0.1090 -284500 27 | CT CT 1 0.1529 224200 28 | NA HA 1 0.1010 -363200 29 | CA HA 1 0.1080 -307100 30 | CA CA 1 0.1380 392500 31 | CA NA 1 0.1340 404200 32 | 33 | CF FC 1 0.1323 369700 34 | CF SO 1 0.1818 197000 35 | SO OS 1 0.1442 533100 36 | NI SO 1 0.1570 311300 37 | 38 | [ angletypes ] 39 | CT CT CT 1 112.7 488.3 40 | CT CT HC 1 110.7 313.8 41 | HC CT HC 1 107.8 276.1 42 | NA CT CT 1 112.7 488.3 43 | CA CA CA 1 120.0 527.2 44 | CA CA HA 1 120.0 292.9 45 | CA CA NA 1 120.0 585.8 46 | CA NA CA 1 120.4 585.8 47 | CA NA CT 1 119.8 585.8 48 | NA CA HA 1 120.0 292.9 49 | NA CT HC 1 109.5 292.9 50 | 51 | OS SO OS 1 118.5 969 52 | OS SO NI 1 113.6 789 53 | CF SO NI 1 100.2 816 54 | SO NI SO 1 125.6 671 55 | FC CF FC 1 107.1 781 56 | FC CF SO 1 111.7 694 57 | CF SO OS 1 102.6 870 58 | 59 | [ dihedraltypes ] 60 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 61 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 62 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 63 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 64 | ; dialkylimidazolium JPCB108:2038(2004) 65 | NA CT CT CT 5 -7.4797 3.1642 -1.2026 0.0000 66 | NA CT CT HC 5 0.0000 0.0000 0.3670 0.0000 67 | ; pyridinium AMBER (cycle) and us 68 | CA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 69 | NA CA CA CA 5 0.0000 30.3340 0.0000 0.0000 70 | HA CA CA NA 5 0.0000 30.3340 0.0000 0.0000 71 | HA CA CA HA 5 0.0000 30.3340 0.0000 0.0000 72 | CA NA CA HA 5 0.0000 12.5520 0.0000 0.0000 73 | CT NA CA HA 5 0.0000 12.5520 0.0000 0.0000 74 | CA NA CA CA 5 0.0000 12.5520 0.0000 0.0000 75 | CT NA CA CA 5 0.0000 12.5520 0.0000 0.0000 76 | HC CT NA CA 5 0.0000 0.0000 0.0000 0.0000 77 | CT CT NA CA 5 0.0000 1.1120 0.0000 0.6900 78 | ; improper pyridinium ring AMBER 79 | CA CA CA HA 5 0.0000 9.2000 0.0000 0.0000 80 | CA CA NA HA 5 0.0000 9.2000 0.0000 0.0000 81 | NA CA CA CT 5 0.0000 8.3700 0.0000 0.0000 82 | ; TFSI 83 | OS SO CF FC 5 0.0000 0.0000 1.4510 0.0000 84 | NI SO CF FC 5 0.0000 0.0000 1.3220 0.0000 85 | OS SO NI SO 5 0.0000 0.0000 -0.0150 0.0000 86 | SO NI SO CF 5 32.7730 -10.4200 -3.1950 0.0000 87 | -------------------------------------------------------------------------------- /topologies/bpytfsi/tfsi.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | TFS 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 NI 1 TFS NI 1 -0.55 14.0067 7 | 2 SO 1 TFS SO 2 0.83 32.06 8 | 3 SO 1 TFS SO 3 0.83 32.06 9 | 4 OS 1 TFS OS 4 -0.47 15.999 10 | 5 OS 1 TFS OS 5 -0.47 15.999 11 | 6 OS 1 TFS OS 6 -0.47 15.999 12 | 7 OS 1 TFS OS 7 -0.47 15.999 13 | 8 CF 1 TFS CF 8 0.35 12.011 14 | 9 CF 1 TFS CF 9 0.35 12.011 15 | 10 FC 1 TFS FC 10 -0.13 18.9984 16 | 11 FC 1 TFS FC 11 -0.13 18.9984 17 | 12 FC 1 TFS FC 12 -0.13 18.9984 18 | 13 FC 1 TFS FC 13 -0.13 18.9984 19 | 14 FC 1 TFS FC 14 -0.13 18.9984 20 | 15 FC 1 TFS FC 15 -0.13 18.9984 21 | 22 | [ bonds ] 23 | 1 2 1 24 | 1 3 1 25 | 2 6 1 26 | 2 7 1 27 | 2 9 1 28 | 3 8 1 29 | 3 4 1 30 | 3 5 1 31 | 8 10 1 32 | 8 11 1 33 | 8 12 1 34 | 9 13 1 35 | 9 14 1 36 | 9 15 1 37 | 38 | [ pairs ] 39 | 2 4 1 40 | 2 5 1 41 | 3 6 1 42 | 3 7 1 43 | 10 4 1 44 | 11 4 1 45 | 12 4 1 46 | 10 5 1 47 | 11 5 1 48 | 12 5 1 49 | 1 10 1 50 | 1 11 1 51 | 1 12 1 52 | 8 2 1 53 | 9 3 1 54 | 13 6 1 55 | 14 6 1 56 | 15 6 1 57 | 13 7 1 58 | 14 7 1 59 | 15 7 1 60 | 13 1 1 61 | 14 1 1 62 | 15 1 1 63 | 64 | [ angles ] 65 | 13 9 14 1 66 | 13 9 15 1 67 | 14 9 15 1 68 | 13 9 2 1 69 | 14 9 2 1 70 | 15 9 2 1 71 | 9 2 6 1 72 | 9 2 7 1 73 | 9 2 1 1 74 | 2 1 3 1 75 | 6 2 1 1 76 | 7 2 1 1 77 | 1 3 4 1 78 | 1 3 5 1 79 | 1 3 8 1 80 | 4 3 8 1 81 | 5 3 8 1 82 | 3 8 10 1 83 | 3 8 11 1 84 | 3 8 12 1 85 | 10 8 11 1 86 | 10 8 12 1 87 | 11 8 12 1 88 | 6 2 7 1 89 | 4 3 5 1 90 | 91 | [ dihedrals ] 92 | ; S-N-S-O 93 | 3 1 2 6 5 94 | 3 1 2 7 5 95 | 2 1 3 4 5 96 | 2 1 3 5 5 97 | ; N-S-C-F 98 | 1 3 8 10 5 99 | 1 3 8 11 5 100 | 1 3 8 12 5 101 | 1 2 9 13 5 102 | 1 2 9 14 5 103 | 1 2 9 15 5 104 | ; O-S-C-F 105 | 5 3 8 10 5 106 | 5 3 8 11 5 107 | 5 3 8 12 5 108 | 4 3 8 10 5 109 | 4 3 8 11 5 110 | 4 3 8 12 5 111 | ; O-S-C-F 112 | 6 2 9 13 5 113 | 6 2 9 14 5 114 | 6 2 9 15 5 115 | 7 2 9 13 5 116 | 7 2 9 14 5 117 | 7 2 9 15 5 118 | ; S-N-S-C 119 | 3 1 2 9 5 120 | 2 1 3 8 5 121 | -------------------------------------------------------------------------------- /topologies/bpytfsi/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "bpy.itp" 3 | #include "tfsi.itp" 4 | 5 | [system] 6 | BPY TFSI 7 | 8 | 9 | [molecules] 10 | BPY 125 11 | TFS 125 12 | 13 | -------------------------------------------------------------------------------- /topologies/py14bf4/bf4.gro: -------------------------------------------------------------------------------- 1 | BF4- 2 | 5 3 | 1BF4 B1 1 1.041 1.600 1.582 4 | 1BF4 F2 2 1.038 1.482 1.659 5 | 1BF4 F3 3 1.169 1.652 1.597 6 | 1BF4 F4 4 0.954 1.693 1.630 7 | 1BF4 F5 5 1.015 1.563 1.448 8 | 3.39953 3.39953 3.39953 9 | -------------------------------------------------------------------------------- /topologies/py14bf4/bf4.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BF4 2 3 | 4 | [ atoms ] 5 | 1 B 1 BF4 B1 1 0.83 10.8100 6 | 2 FB 1 BF4 F2 2 -0.39 18.9984 7 | 3 FB 1 BF4 F3 3 -0.39 18.9984 8 | 4 FB 1 BF4 F4 4 -0.39 18.9984 9 | 5 FB 1 BF4 F5 5 -0.39 18.9984 10 | 11 | [ bonds ] 12 | 1 2 1 13 | 1 3 1 14 | 1 4 1 15 | 1 5 1 16 | 17 | [ angles ] 18 | 2 1 3 1 19 | 2 1 4 1 20 | 2 1 5 1 21 | 3 1 5 1 22 | 3 1 4 1 23 | 4 1 5 1 24 | -------------------------------------------------------------------------------- /topologies/py14bf4/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ;pyrrolidinium JPCB108(2004)16893 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NT 7 14.007 0.12 A 0.325 0.71128 10 | ; tetrafluoroborate 11 | B 5 10.811 0.96 A 0.358 0.3975 12 | FB 9 18.998 -0.49 A 0.312 0.2552 13 | 14 | [ bondtypes ] 15 | HC CT 1 0.1090 -284500 ; - 16 | CT CT 1 0.1529 224200 ; 17 | NT CT 1 0.1471 307100.0 18 | ; tetrafluoroborate 19 | B FB 1 0.1394 323500 20 | 21 | [ angletypes ] 22 | CT CT CT 1 112.7 488.3 23 | CT CT HC 1 110.7 313.8 24 | HC CT HC 1 107.8 276.1 25 | NT CT CT 1 109.5 669.4 26 | CT NT CT 1 109.5 418.4 27 | HC CT NT 1 109.5 209.2 28 | ; tetrafluoroborate 29 | FB B FB 1 109.5 669.5 30 | 31 | [ dihedraltypes ] 32 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 33 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 34 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 35 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 36 | ;pyrrolidilium 37 | HC CT CT NT 5 -4.2384 -2.9665 1.9790 0.0000 38 | CT CT CT NT 5 10.0081 -2.8200 2.3012 0.0000 39 | CT NT CT CT 5 1.7405 -0.5356 2.9079 0.0000 40 | HC CT NT CT 5 0.0000 0.0000 2.3430 0.0000 41 | 42 | -------------------------------------------------------------------------------- /topologies/py14bf4/pyr.gro: -------------------------------------------------------------------------------- 1 | PYR+ 2 | 30 3 | 1PYR N1 1 0.000 0.000 0.000 4 | 1PYR C2 2 0.000 0.000 0.147 5 | 1PYR C3 3 0.139 0.000 -0.049 6 | 1PYR C4 4 0.144 0.000 0.198 7 | 1PYR C5 5 0.235 0.000 0.070 8 | 1PYR C6 6 -0.069 -0.120 -0.049 9 | 1PYR C7 7 -0.069 0.120 -0.049 10 | 1PYR H8 8 -0.051 -0.089 0.183 11 | 1PYR H9 9 -0.051 0.089 0.183 12 | 1PYR H10 10 0.156 -0.089 -0.110 13 | 1PYR H11 11 0.156 0.089 -0.110 14 | 1PYR H12 12 0.163 -0.088 0.259 15 | 1PYR H13 13 0.163 0.088 0.259 16 | 1PYR H14 14 0.299 -0.088 0.068 17 | 1PYR H15 15 0.299 0.088 0.068 18 | 1PYR H16 16 -0.172 -0.120 -0.013 19 | 1PYR H17 17 -0.069 -0.120 -0.158 20 | 1PYR H18 18 -0.018 -0.209 -0.013 21 | 1PYR H19 19 -0.069 0.120 -0.158 22 | 1PYR H20 20 -0.172 0.120 -0.013 23 | 1PYR C21 21 0.003 0.245 0.002 24 | 1PYR H22 22 0.105 0.245 -0.035 25 | 1PYR H23 23 0.003 0.245 0.111 26 | 1PYR C24 24 -0.069 0.370 -0.049 27 | 1PYR H25 25 -0.172 0.370 -0.013 28 | 1PYR H26 26 -0.069 0.370 -0.158 29 | 1PYR C27 27 0.003 0.495 0.002 30 | 1PYR H28 28 0.105 0.495 -0.035 31 | 1PYR H29 29 0.003 0.495 0.111 32 | 1PYR H30 30 -0.049 0.584 -0.035 33 | 3.39953 3.39953 3.39953 34 | -------------------------------------------------------------------------------- /topologies/py14bf4/pyr.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | PYR 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 NT 1 PYR N1 0 0.0876 14.0067 7 | 2 CT 1 PYR C2 1 -0.1241 12.011 8 | 3 CT 1 PYR C3 2 -0.1241 12.011 9 | 4 CT 1 PYR C4 3 0.0073 12.011 10 | 5 CT 1 PYR C5 4 0.0073 12.011 11 | 6 CT 1 PYR C6 5 -0.1241 12.011 12 | 7 CT 1 PYR C7 6 -0.1241 12.011 13 | 8 HC 1 PYR H8 7 0.0949 1.008 14 | 9 HC 1 PYR H9 8 0.0949 1.008 15 | 10 HC 1 PYR H10 9 0.0949 1.008 16 | 11 HC 1 PYR H11 10 0.0949 1.008 17 | 12 HC 1 PYR H12 11 0.0438 1.008 18 | 13 HC 1 PYR H13 12 0.0438 1.008 19 | 14 HC 1 PYR H14 13 0.0438 1.008 20 | 15 HC 1 PYR H15 14 0.0438 1.008 21 | 16 HC 1 PYR H16 15 0.0949 1.008 22 | 17 HC 1 PYR H17 16 0.0949 1.008 23 | 18 HC 1 PYR H18 17 0.0949 1.008 24 | 19 HC 1 PYR H19 18 0.0949 1.008 25 | 20 HC 1 PYR H20 19 0.0949 1.008 26 | 21 CT 1 PYR C21 20 0.0073 12.011 27 | 22 HC 1 PYR H22 21 0.0438 1.008 28 | 23 HC 1 PYR H23 22 0.0438 1.008 29 | 24 CT 1 PYR C24 23 -0.12 12.011 30 | 25 HC 1 PYR H25 24 0.06 1.008 31 | 26 HC 1 PYR H26 25 0.06 1.008 32 | 27 CT 1 PYR C27 26 -0.18 12.011 33 | 28 HC 1 PYR H28 27 0.06 1.008 34 | 29 HC 1 PYR H29 28 0.06 1.008 35 | 30 HC 1 PYR H30 29 0.06 1.008 36 | 37 | [ pairs ] 38 | 1 4 1 39 | 1 14 1 40 | 1 15 1 41 | 1 12 1 42 | 1 13 1 43 | 1 24 1 44 | 1 22 1 45 | 1 23 1 46 | 47 | 2 3 1 48 | 2 14 1 49 | 2 15 1 50 | 2 10 1 51 | 2 11 1 52 | 2 16 1 53 | 2 17 1 54 | 2 18 1 55 | 2 19 1 56 | 2 20 1 57 | 2 21 1 58 | 59 | 3 16 1 60 | 3 17 1 61 | 3 18 1 62 | 3 12 1 63 | 3 13 1 64 | 3 8 1 65 | 3 9 1 66 | 3 21 1 67 | 3 19 1 68 | 3 20 1 69 | 70 | 4 10 1 71 | 4 11 1 72 | 4 6 1 73 | 4 7 1 74 | 75 | 5 8 1 76 | 5 9 1 77 | 5 6 1 78 | 5 7 1 79 | 5 8 1 80 | 5 9 1 81 | 82 | 6 10 1 83 | 6 11 1 84 | 6 21 1 85 | 6 8 1 86 | 6 9 1 87 | 6 20 1 88 | 6 19 1 89 | 90 | 7 17 1 91 | 7 18 1 92 | 7 16 1 93 | 7 10 1 94 | 7 11 1 95 | 7 8 1 96 | 7 9 1 97 | 7 25 1 98 | 7 26 1 99 | 7 27 1 100 | 101 | 8 12 1 102 | 8 13 1 103 | 104 | 9 12 1 105 | 9 13 1 106 | 107 | 10 14 1 108 | 10 15 1 109 | 110 | 11 14 1 111 | 11 15 1 112 | 113 | 12 14 1 114 | 12 15 1 115 | 116 | 13 14 1 117 | 13 15 1 118 | 119 | 19 22 1 120 | 19 23 1 121 | 19 24 1 122 | 123 | 20 22 1 124 | 20 23 1 125 | 20 24 1 126 | 127 | 21 28 1 128 | 21 29 1 129 | 21 30 1 130 | 131 | 22 25 1 132 | 22 26 1 133 | 22 27 1 134 | 135 | 23 25 1 136 | 23 26 1 137 | 23 27 1 138 | 139 | 25 28 1 140 | 25 29 1 141 | 25 30 1 142 | 143 | 26 28 1 144 | 26 29 1 145 | 26 30 1 146 | 147 | [ bonds ] 148 | 1 2 1 149 | 1 3 1 150 | 1 6 1 151 | 1 7 1 152 | 2 4 1 153 | 2 8 1 154 | 2 9 1 155 | 4 12 1 156 | 4 13 1 157 | 4 5 1 158 | 5 14 1 159 | 5 15 1 160 | 5 3 1 161 | 3 10 1 162 | 3 11 1 163 | 6 16 1 164 | 6 17 1 165 | 6 18 1 166 | 7 19 1 167 | 7 20 1 168 | 7 21 1 169 | 21 22 1 170 | 21 23 1 171 | 21 24 1 172 | 24 25 1 173 | 24 26 1 174 | 24 27 1 175 | 27 28 1 176 | 27 29 1 177 | 27 30 1 178 | 179 | [ angles ] 180 | ; ai aj ak funct c0 c1 c2 c3 181 | 2 4 5 1 182 | 3 5 4 1 183 | 7 21 24 1 184 | 21 24 27 1 185 | 186 | 2 4 12 1 187 | 2 4 13 1 188 | 4 2 8 1 189 | 4 2 9 1 190 | 4 5 14 1 191 | 4 5 15 1 192 | 5 4 12 1 193 | 5 4 13 1 194 | 5 3 10 1 195 | 5 3 11 1 196 | 3 5 14 1 197 | 3 5 14 1 198 | 7 21 22 1 199 | 7 21 23 1 200 | 21 7 19 1 201 | 21 7 20 1 202 | 21 24 25 1 203 | 21 24 26 1 204 | 24 21 22 1 205 | 24 21 23 1 206 | 24 27 28 1 207 | 24 27 29 1 208 | 24 27 30 1 209 | 27 24 25 1 210 | 27 24 26 1 211 | 212 | 8 2 9 1 213 | 12 4 13 1 214 | 14 5 15 1 215 | 10 3 11 1 216 | 16 6 17 1 217 | 16 6 18 1 218 | 17 6 18 1 219 | 19 7 20 1 220 | 22 21 23 1 221 | 25 24 26 1 222 | 28 27 29 1 223 | 28 27 30 1 224 | 29 27 30 1 225 | 226 | 1 3 5 1 227 | 1 2 4 1 228 | 1 7 21 1 229 | 230 | 2 1 3 1 231 | 6 1 7 1 232 | 3 1 7 1 233 | 2 1 6 1 234 | 2 1 7 1 235 | 3 1 6 1 236 | 237 | 10 3 1 1 238 | 11 3 1 1 239 | 8 2 1 1 240 | 9 2 1 1 241 | 16 6 1 1 242 | 17 6 1 1 243 | 18 6 1 1 244 | 19 7 1 1 245 | 20 7 1 1 246 | 247 | [ dihedrals ] 248 | ;HC-CT-CT-HC 249 | 9 2 4 12 5 250 | 9 2 4 13 5 251 | 8 2 4 12 5 252 | 8 2 4 13 5 253 | 12 4 5 14 5 254 | 12 4 5 15 5 255 | 13 4 5 14 5 256 | 13 4 5 15 5 257 | 25 24 27 28 5 258 | 25 24 27 29 5 259 | 25 24 27 30 5 260 | 26 24 27 28 5 261 | 26 24 27 29 5 262 | 26 24 27 30 5 263 | 14 5 3 10 5 264 | 14 5 3 11 5 265 | 15 5 3 10 5 266 | 15 5 3 11 5 267 | 19 7 21 23 5 268 | 19 7 21 22 5 269 | 20 7 21 23 5 270 | 20 7 21 22 5 271 | 22 21 24 25 5 272 | 22 21 24 26 5 273 | 23 21 24 25 5 274 | 23 21 24 26 5 275 | ;CT-CT-CT-HC 276 | 2 4 5 14 5 277 | 2 4 5 15 5 278 | 4 5 3 10 5 279 | 4 5 3 11 5 280 | 3 5 4 12 5 281 | 3 5 4 13 5 282 | 5 4 2 8 5 283 | 5 4 2 9 5 284 | 7 21 24 25 5 285 | 7 21 24 26 5 286 | 21 24 27 28 5 287 | 21 24 27 29 5 288 | 21 24 27 30 5 289 | 27 24 21 22 5 290 | 27 24 21 23 5 291 | 24 21 7 19 5 292 | 24 21 7 20 5 293 | ;CT-CT-CT-CT 294 | 2 4 5 3 5 295 | 7 21 24 27 5 296 | ;HC-CT-CT-NT 297 | 14 5 3 1 5 298 | 15 5 3 1 5 299 | 12 4 2 1 5 300 | 13 4 2 1 5 301 | 22 21 7 1 5 302 | 23 21 7 1 5 303 | ;CT-CT-CT-NT 304 | 5 4 2 1 5 305 | 4 5 3 1 5 306 | 24 21 7 1 5 307 | ;CT-NT-CT-CT 308 | 2 1 3 5 5 309 | 2 1 7 21 5 310 | 3 1 2 4 5 311 | 3 1 7 21 5 312 | 7 1 3 5 5 313 | 7 1 2 4 5 314 | 6 1 2 4 5 315 | 6 1 3 5 5 316 | 6 1 7 21 5 317 | ;HC-CT-NT-CT 318 | 8 2 1 6 5 319 | 9 2 1 6 5 320 | 8 2 1 3 5 321 | 9 2 1 3 5 322 | 8 2 1 7 5 323 | 9 2 1 7 5 324 | 10 3 1 2 5 325 | 11 3 1 2 5 326 | 10 3 1 6 5 327 | 11 3 1 6 5 328 | 10 3 1 7 5 329 | 11 3 1 7 5 330 | 19 7 1 2 5 331 | 20 7 1 2 5 332 | 19 7 1 3 5 333 | 20 7 1 3 5 334 | 19 7 1 6 5 335 | 20 7 1 6 5 336 | 16 6 1 2 5 337 | 17 6 1 2 5 338 | 18 6 1 2 5 339 | 16 6 1 3 5 340 | 17 6 1 3 5 341 | 18 6 1 3 5 342 | 16 6 1 7 5 343 | 17 6 1 7 5 344 | 18 6 1 7 5 345 | -------------------------------------------------------------------------------- /topologies/py14bf4/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "pyr.itp" 3 | #include "bf4.itp" 4 | 5 | [system] 6 | PYR BF4 7 | 8 | [molecules] 9 | PYR 150 10 | BF4 150 11 | -------------------------------------------------------------------------------- /topologies/py14cl/chloride.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | CL 1 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CL 1 CL CL 1 -0.71 35.453 7 | -------------------------------------------------------------------------------- /topologies/py14cl/cl.gro: -------------------------------------------------------------------------------- 1 | CL- 2 | 1 3 | 1CL CL1 1 0.500 0.500 0.300 4 | 3.39953 3.39953 3.39953 5 | -------------------------------------------------------------------------------- /topologies/py14cl/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ;pyrrolidinium JPCB108(2004)16893 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NT 7 14.007 0.12 A 0.325 0.71128 10 | 11 | ;Cl 12 | CL 17 35.453 -1.000 A 0.365 0.8300 13 | 14 | [ bondtypes ] 15 | ; this is for pyrrolidinium 16 | HC CT 1 0.1090 -284500 ; - 17 | CT CT 1 0.1529 224200 ; 18 | NT CT 1 0.1471 307100.0 19 | 20 | [ angletypes ] 21 | CT CT CT 1 112.7 488.3 22 | CT CT HC 1 110.7 313.8 23 | HC CT HC 1 107.8 276.1 24 | NT CT CT 1 109.5 669.4 25 | CT NT CT 1 109.5 418.4 26 | HC CT NT 1 109.5 209.2 27 | 28 | [ dihedraltypes ] 29 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 30 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 31 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 32 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 33 | ;pyrrolidilium 34 | HC CT CT NT 5 -4.2384 -2.9665 1.9790 0.0000 35 | CT CT CT NT 5 10.0081 -2.8200 2.3012 0.0000 36 | CT NT CT CT 5 1.7405 -0.5356 2.9079 0.0000 37 | HC CT NT CT 5 0.0000 0.0000 2.3430 0.0000 38 | -------------------------------------------------------------------------------- /topologies/py14cl/pyr.gro: -------------------------------------------------------------------------------- 1 | PYR+ 2 | 30 3 | 1PYR N1 1 0.000 0.000 0.000 4 | 1PYR C2 2 0.000 0.000 0.147 5 | 1PYR C3 3 0.139 0.000 -0.049 6 | 1PYR C4 4 0.144 0.000 0.198 7 | 1PYR C5 5 0.235 0.000 0.070 8 | 1PYR C6 6 -0.069 -0.120 -0.049 9 | 1PYR C7 7 -0.069 0.120 -0.049 10 | 1PYR H8 8 -0.051 -0.089 0.183 11 | 1PYR H9 9 -0.051 0.089 0.183 12 | 1PYR H10 10 0.156 -0.089 -0.110 13 | 1PYR H11 11 0.156 0.089 -0.110 14 | 1PYR H12 12 0.163 -0.088 0.259 15 | 1PYR H13 13 0.163 0.088 0.259 16 | 1PYR H14 14 0.299 -0.088 0.068 17 | 1PYR H15 15 0.299 0.088 0.068 18 | 1PYR H16 16 -0.172 -0.120 -0.013 19 | 1PYR H17 17 -0.069 -0.120 -0.158 20 | 1PYR H18 18 -0.018 -0.209 -0.013 21 | 1PYR H19 19 -0.069 0.120 -0.158 22 | 1PYR H20 20 -0.172 0.120 -0.013 23 | 1PYR C21 21 0.003 0.245 0.002 24 | 1PYR H22 22 0.105 0.245 -0.035 25 | 1PYR H23 23 0.003 0.245 0.111 26 | 1PYR C24 24 -0.069 0.370 -0.049 27 | 1PYR H25 25 -0.172 0.370 -0.013 28 | 1PYR H26 26 -0.069 0.370 -0.158 29 | 1PYR C27 27 0.003 0.495 0.002 30 | 1PYR H28 28 0.105 0.495 -0.035 31 | 1PYR H29 29 0.003 0.495 0.111 32 | 1PYR H30 30 -0.049 0.584 -0.035 33 | 3.39953 3.39953 3.39953 34 | -------------------------------------------------------------------------------- /topologies/py14cl/pyr.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | PYR 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 NT 1 PYR N1 0 0.0852 14.0067 7 | 2 CT 1 PYR C2 1 -0.1207 12.011 8 | 3 CT 1 PYR C3 2 -0.1207 12.011 9 | 4 CT 1 PYR C4 3 0.0071 12.011 10 | 5 CT 1 PYR C5 4 0.0071 12.011 11 | 6 CT 1 PYR C6 5 -0.1207 12.011 12 | 7 CT 1 PYR C7 6 -0.1207 12.011 13 | 8 HC 1 PYR H8 7 0.0923 1.008 14 | 9 HC 1 PYR H9 8 0.0923 1.008 15 | 10 HC 1 PYR H10 9 0.0923 1.008 16 | 11 HC 1 PYR H11 10 0.0923 1.008 17 | 12 HC 1 PYR H12 11 0.0426 1.008 18 | 13 HC 1 PYR H13 12 0.0426 1.008 19 | 14 HC 1 PYR H14 13 0.0426 1.008 20 | 15 HC 1 PYR H15 14 0.0426 1.008 21 | 16 HC 1 PYR H16 15 0.0923 1.008 22 | 17 HC 1 PYR H17 16 0.0923 1.008 23 | 18 HC 1 PYR H18 17 0.0923 1.008 24 | 19 HC 1 PYR H19 18 0.0923 1.008 25 | 20 HC 1 PYR H20 19 0.0923 1.008 26 | 21 CT 1 PYR C21 20 0.0071 12.011 27 | 22 HC 1 PYR H22 21 0.0426 1.008 28 | 23 HC 1 PYR H23 22 0.0426 1.008 29 | 24 CT 1 PYR C24 23 -0.12 12.011 30 | 25 HC 1 PYR H25 24 0.06 1.008 31 | 26 HC 1 PYR H26 25 0.06 1.008 32 | 27 CT 1 PYR C27 26 -0.18 12.011 33 | 28 HC 1 PYR H28 27 0.06 1.008 34 | 29 HC 1 PYR H29 28 0.06 1.008 35 | 30 HC 1 PYR H30 29 0.06 1.008 36 | 37 | [ pairs ] 38 | 1 4 1 39 | 1 14 1 40 | 1 15 1 41 | 1 12 1 42 | 1 13 1 43 | 1 24 1 44 | 1 22 1 45 | 1 23 1 46 | 47 | 2 3 1 48 | 2 14 1 49 | 2 15 1 50 | 2 10 1 51 | 2 11 1 52 | 2 16 1 53 | 2 17 1 54 | 2 18 1 55 | 2 19 1 56 | 2 20 1 57 | 2 21 1 58 | 59 | 3 16 1 60 | 3 17 1 61 | 3 18 1 62 | 3 12 1 63 | 3 13 1 64 | 3 8 1 65 | 3 9 1 66 | 3 21 1 67 | 3 19 1 68 | 3 20 1 69 | 70 | 4 10 1 71 | 4 11 1 72 | 4 6 1 73 | 4 7 1 74 | 75 | 5 8 1 76 | 5 9 1 77 | 5 6 1 78 | 5 7 1 79 | 5 8 1 80 | 5 9 1 81 | 82 | 6 10 1 83 | 6 11 1 84 | 6 21 1 85 | 6 8 1 86 | 6 9 1 87 | 6 20 1 88 | 6 19 1 89 | 90 | 7 17 1 91 | 7 18 1 92 | 7 16 1 93 | 7 10 1 94 | 7 11 1 95 | 7 8 1 96 | 7 9 1 97 | 7 25 1 98 | 7 26 1 99 | 7 27 1 100 | 101 | 8 12 1 102 | 8 13 1 103 | 104 | 9 12 1 105 | 9 13 1 106 | 107 | 10 14 1 108 | 10 15 1 109 | 110 | 11 14 1 111 | 11 15 1 112 | 113 | 12 14 1 114 | 12 15 1 115 | 116 | 13 14 1 117 | 13 15 1 118 | 119 | 19 22 1 120 | 19 23 1 121 | 19 24 1 122 | 123 | 20 22 1 124 | 20 23 1 125 | 20 24 1 126 | 127 | 21 28 1 128 | 21 29 1 129 | 21 30 1 130 | 131 | 22 25 1 132 | 22 26 1 133 | 22 27 1 134 | 135 | 23 25 1 136 | 23 26 1 137 | 23 27 1 138 | 139 | 25 28 1 140 | 25 29 1 141 | 25 30 1 142 | 143 | 26 28 1 144 | 26 29 1 145 | 26 30 1 146 | 147 | [ bonds ] 148 | 1 2 1 149 | 1 3 1 150 | 1 6 1 151 | 1 7 1 152 | 2 4 1 153 | 2 8 1 154 | 2 9 1 155 | 4 12 1 156 | 4 13 1 157 | 4 5 1 158 | 5 14 1 159 | 5 15 1 160 | 5 3 1 161 | 3 10 1 162 | 3 11 1 163 | 6 16 1 164 | 6 17 1 165 | 6 18 1 166 | 7 19 1 167 | 7 20 1 168 | 7 21 1 169 | 21 22 1 170 | 21 23 1 171 | 21 24 1 172 | 24 25 1 173 | 24 26 1 174 | 24 27 1 175 | 27 28 1 176 | 27 29 1 177 | 27 30 1 178 | 179 | [ angles ] 180 | ; ai aj ak funct c0 c1 c2 c3 181 | 2 4 5 1 182 | 3 5 4 1 183 | 7 21 24 1 184 | 21 24 27 1 185 | 186 | 2 4 12 1 187 | 2 4 13 1 188 | 4 2 8 1 189 | 4 2 9 1 190 | 4 5 14 1 191 | 4 5 15 1 192 | 5 4 12 1 193 | 5 4 13 1 194 | 5 3 10 1 195 | 5 3 11 1 196 | 3 5 14 1 197 | 3 5 14 1 198 | 7 21 22 1 199 | 7 21 23 1 200 | 21 7 19 1 201 | 21 7 20 1 202 | 21 24 25 1 203 | 21 24 26 1 204 | 24 21 22 1 205 | 24 21 23 1 206 | 24 27 28 1 207 | 24 27 29 1 208 | 24 27 30 1 209 | 27 24 25 1 210 | 27 24 26 1 211 | 212 | 8 2 9 1 213 | 12 4 13 1 214 | 14 5 15 1 215 | 10 3 11 1 216 | 16 6 17 1 217 | 16 6 18 1 218 | 17 6 18 1 219 | 19 7 20 1 220 | 22 21 23 1 221 | 25 24 26 1 222 | 28 27 29 1 223 | 28 27 30 1 224 | 29 27 30 1 225 | 226 | 1 3 5 1 227 | 1 2 4 1 228 | 1 7 21 1 229 | 230 | 2 1 3 1 231 | 6 1 7 1 232 | 3 1 7 1 233 | 2 1 6 1 234 | 2 1 7 1 235 | 3 1 6 1 236 | 237 | 10 3 1 1 238 | 11 3 1 1 239 | 8 2 1 1 240 | 9 2 1 1 241 | 16 6 1 1 242 | 17 6 1 1 243 | 18 6 1 1 244 | 19 7 1 1 245 | 20 7 1 1 246 | 247 | [ dihedrals ] 248 | ;HC-CT-CT-HC 249 | 9 2 4 12 5 250 | 9 2 4 13 5 251 | 8 2 4 12 5 252 | 8 2 4 13 5 253 | 12 4 5 14 5 254 | 12 4 5 15 5 255 | 13 4 5 14 5 256 | 13 4 5 15 5 257 | 25 24 27 28 5 258 | 25 24 27 29 5 259 | 25 24 27 30 5 260 | 26 24 27 28 5 261 | 26 24 27 29 5 262 | 26 24 27 30 5 263 | 14 5 3 10 5 264 | 14 5 3 11 5 265 | 15 5 3 10 5 266 | 15 5 3 11 5 267 | 19 7 21 23 5 268 | 19 7 21 22 5 269 | 20 7 21 23 5 270 | 20 7 21 22 5 271 | 22 21 24 25 5 272 | 22 21 24 26 5 273 | 23 21 24 25 5 274 | 23 21 24 26 5 275 | ;CT-CT-CT-HC 276 | 2 4 5 14 5 277 | 2 4 5 15 5 278 | 4 5 3 10 5 279 | 4 5 3 11 5 280 | 3 5 4 12 5 281 | 3 5 4 13 5 282 | 5 4 2 8 5 283 | 5 4 2 9 5 284 | 7 21 24 25 5 285 | 7 21 24 26 5 286 | 21 24 27 28 5 287 | 21 24 27 29 5 288 | 21 24 27 30 5 289 | 27 24 21 22 5 290 | 27 24 21 23 5 291 | 24 21 7 19 5 292 | 24 21 7 20 5 293 | ;CT-CT-CT-CT 294 | 2 4 5 3 5 295 | 7 21 24 27 5 296 | ;HC-CT-CT-NT 297 | 14 5 3 1 5 298 | 15 5 3 1 5 299 | 12 4 2 1 5 300 | 13 4 2 1 5 301 | 22 21 7 1 5 302 | 23 21 7 1 5 303 | ;CT-CT-CT-NT 304 | 5 4 2 1 5 305 | 4 5 3 1 5 306 | 24 21 7 1 5 307 | ;CT-NT-CT-CT 308 | 2 1 3 5 5 309 | 2 1 7 21 5 310 | 3 1 2 4 5 311 | 3 1 7 21 5 312 | 7 1 3 5 5 313 | 7 1 2 4 5 314 | 6 1 2 4 5 315 | 6 1 3 5 5 316 | 6 1 7 21 5 317 | ;HC-CT-NT-CT 318 | 8 2 1 6 5 319 | 9 2 1 6 5 320 | 8 2 1 3 5 321 | 9 2 1 3 5 322 | 8 2 1 7 5 323 | 9 2 1 7 5 324 | 10 3 1 2 5 325 | 11 3 1 2 5 326 | 10 3 1 6 5 327 | 11 3 1 6 5 328 | 10 3 1 7 5 329 | 11 3 1 7 5 330 | 19 7 1 2 5 331 | 20 7 1 2 5 332 | 19 7 1 3 5 333 | 20 7 1 3 5 334 | 19 7 1 6 5 335 | 20 7 1 6 5 336 | 16 6 1 2 5 337 | 17 6 1 2 5 338 | 18 6 1 2 5 339 | 16 6 1 3 5 340 | 17 6 1 3 5 341 | 18 6 1 3 5 342 | 16 6 1 7 5 343 | 17 6 1 7 5 344 | 18 6 1 7 5 345 | -------------------------------------------------------------------------------- /topologies/py14cl/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "pyr.itp" 3 | #include "chloride.itp" 4 | 5 | [system] 6 | PYR CL 7 | 8 | 9 | [molecules] 10 | PYR 175 11 | CL 175 12 | -------------------------------------------------------------------------------- /topologies/py14dca/dca.gro: -------------------------------------------------------------------------------- 1 | DCA- 2 | 5 3 | 1DCA N31 1 0.000 0.000 0.000 4 | 1DCA CZ2 2 0.131 0.000 0.000 5 | 1DCA NZ3 3 0.246 0.010 0.000 6 | 1DCA CZ4 4 -0.063 -0.115 0.000 7 | 1DCA NZ5 5 -0.126 -0.211 0.000 8 | 3.39953 3.39953 3.39953 9 | -------------------------------------------------------------------------------- /topologies/py14dca/dca.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | DCA 3 3 | 4 | [ atoms ] 5 | ;nr type resnr residue atom cgnr charge mass 6 | 1 N3 1 DCA N31 1 -0.57 14.00027 7 | 2 CZ 1 DCA CZ2 2 0.48 12.011 8 | 3 NZ 1 DCA NZ3 3 -0.57 14.00027 9 | 4 CZ 1 DCA CZ4 4 0.48 12.011 10 | 5 NZ 1 DCA NZ5 5 -0.57 14.00027 11 | 12 | [ pairs ] 13 | 2 5 1 14 | 3 4 1 15 | 16 | [ bonds ] 17 | 1 2 1 18 | 1 4 1 19 | 2 3 1 20 | 4 5 1 21 | 22 | [ angles ] 23 | 2 1 4 1 24 | 1 2 3 1 25 | 1 4 5 1 26 | 27 | [dihedrals] 28 | 4 1 2 3 5 29 | 2 1 4 5 5 30 | -------------------------------------------------------------------------------- /topologies/py14dca/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ;pyrrolidinium JPCB108(2004)16893 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NT 7 14.007 0.12 A 0.325 0.71128 10 | ; dicyanamide JPCB110(2006)19586 11 | N3 7 14.00027 -0.76 A 0.325 0.71128 12 | CZ 6 12.011 0.64 A 0.330 0.27614 13 | NZ 7 14.00027 -0.76 A 0.320 0.71128 14 | 15 | [ bondtypes ] 16 | ; this is for pyrrolidinium 17 | HC CT 1 0.1090 -284500 ; - 18 | CT CT 1 0.1529 224200 ; 19 | NT CT 1 0.1471 307100.0 20 | ; dca- 21 | N3 CZ 1 0.1310 420600 22 | CZ NZ 1 0.1157 774600 23 | 24 | [ angletypes ] 25 | CT CT CT 1 112.7 488.3 26 | CT CT HC 1 110.7 313.8 27 | HC CT HC 1 107.8 276.1 28 | NT CT CT 1 109.5 669.4 29 | CT NT CT 1 109.5 418.4 30 | HC CT NT 1 109.5 209.2 31 | ; dca- 32 | CZ N3 CZ 1 118.5 362.0 33 | N3 CZ NZ 1 175.2 425.0 34 | 35 | [ dihedraltypes ] 36 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 37 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 38 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 39 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 40 | ;pyrrolidilium 41 | HC CT CT NT 5 -4.2384 -2.9665 1.9790 0.0000 42 | CT CT CT NT 5 10.0081 -2.8200 2.3012 0.0000 43 | CT NT CT CT 5 1.7405 -0.5356 2.9079 0.0000 44 | HC CT NT CT 5 0.0000 0.0000 2.3430 0.0000 45 | ; dca- CL&P 46 | NZ CZ N3 CZ 5 4.0800 0.0000 0.0000 0.0000 47 | -------------------------------------------------------------------------------- /topologies/py14dca/pyr.gro: -------------------------------------------------------------------------------- 1 | PYR+ 2 | 30 3 | 1PYR N1 1 0.000 0.000 0.000 4 | 1PYR C2 2 0.000 0.000 0.147 5 | 1PYR C3 3 0.139 0.000 -0.049 6 | 1PYR C4 4 0.144 0.000 0.198 7 | 1PYR C5 5 0.235 0.000 0.070 8 | 1PYR C6 6 -0.069 -0.120 -0.049 9 | 1PYR C7 7 -0.069 0.120 -0.049 10 | 1PYR H8 8 -0.051 -0.089 0.183 11 | 1PYR H9 9 -0.051 0.089 0.183 12 | 1PYR H10 10 0.156 -0.089 -0.110 13 | 1PYR H11 11 0.156 0.089 -0.110 14 | 1PYR H12 12 0.163 -0.088 0.259 15 | 1PYR H13 13 0.163 0.088 0.259 16 | 1PYR H14 14 0.299 -0.088 0.068 17 | 1PYR H15 15 0.299 0.088 0.068 18 | 1PYR H16 16 -0.172 -0.120 -0.013 19 | 1PYR H17 17 -0.069 -0.120 -0.158 20 | 1PYR H18 18 -0.018 -0.209 -0.013 21 | 1PYR H19 19 -0.069 0.120 -0.158 22 | 1PYR H20 20 -0.172 0.120 -0.013 23 | 1PYR C21 21 0.003 0.245 0.002 24 | 1PYR H22 22 0.105 0.245 -0.035 25 | 1PYR H23 23 0.003 0.245 0.111 26 | 1PYR C24 24 -0.069 0.370 -0.049 27 | 1PYR H25 25 -0.172 0.370 -0.013 28 | 1PYR H26 26 -0.069 0.370 -0.158 29 | 1PYR C27 27 0.003 0.495 0.002 30 | 1PYR H28 28 0.105 0.495 -0.035 31 | 1PYR H29 29 0.003 0.495 0.111 32 | 1PYR H30 30 -0.049 0.584 -0.035 33 | 3.39953 3.39953 3.39953 34 | -------------------------------------------------------------------------------- /topologies/py14dca/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "pyr.itp" 3 | #include "dca.itp" 4 | 5 | [system] 6 | PYR DCA 7 | 8 | 9 | [molecules] 10 | PYR 150 11 | DCA 150 12 | -------------------------------------------------------------------------------- /topologies/py14fsi/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ;pyrrolidinium JPCB108(2004)16893 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NT 7 14.007 0.12 A 0.325 0.71128 10 | 11 | ;FSI 12 | OB 8 15.999 -0.53 A 0.296 0.87864 13 | NB 7 14.000 -0.66 A 0.325 0.71128 14 | FB 9 18.998 -0.13 A 0.295 0.22175 15 | SB 16 32.066 1.02 A 0.355 1.04600 16 | 17 | [ bondtypes ] 18 | HC CT 1 0.1090 -284500 ; - 19 | CT CT 1 0.1529 224200 ; 20 | NT CT 1 0.1471 307100.0 21 | ;FSI 22 | FB SB 1 0.1575 187900 23 | SB OB 1 0.1437 533100 24 | NB SB 1 0.1570 313700 25 | 26 | [ angletypes ] 27 | CT CT CT 1 112.7 488.3 28 | CT CT HC 1 110.7 313.8 29 | HC CT HC 1 107.8 276.1 30 | NT CT CT 1 109.5 669.4 31 | CT NT CT 1 109.5 418.4 32 | HC CT NT 1 109.5 209.2 33 | ;FSI 34 | OB SB OB 1 118.5 969.0 35 | FB SB OB 1 104.1 1077.0 36 | FB SB NB 1 103.0 902.0 37 | NB SB OB 1 113.6 789.0 38 | SB NB SB 1 125.6 671.0 39 | 40 | [ dihedraltypes ] 41 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 42 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 43 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 44 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 45 | ;pyrrolidilium 46 | HC CT CT NT 5 -4.2384 -2.9665 1.9790 0.0000 47 | CT CT CT NT 5 10.0081 -2.8200 2.3012 0.0000 48 | CT NT CT CT 5 1.7405 -0.5356 2.9079 0.0000 49 | HC CT NT CT 5 0.0000 0.0000 2.3430 0.0000 50 | ;FSI 51 | FB SB NB SB 5 13.4514 -12.3373 -8.4874 -2.8654 52 | OB SB NB SB 5 0.0000 0.0000 -0.0150 0.0000 53 | -------------------------------------------------------------------------------- /topologies/py14fsi/fsi.gro: -------------------------------------------------------------------------------- 1 | FSI- 2 | 9 3 | 1FSI F1 1 0.000 0.000 0.000 4 | 2FSI S2 2 0.000 0.000 0.158 5 | 3FSI N3 3 0.146 0.000 0.191 6 | 4FSI O4 4 -0.070 0.121 0.193 7 | 5FSI O5 5 -0.070 -0.121 0.193 8 | 6FSI S6 6 0.219 0.130 0.208 9 | 7FSI O7 7 0.147 0.218 0.119 10 | 8FSI O6 8 0.353 0.096 0.167 11 | 9FSI F7 9 0.202 0.161 0.362 12 | 3.39953 3.39953 3.39953 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /topologies/py14fsi/fsi.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | FSI 5 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 FB 1 FSI F1 0 -0.13 18.998 7 | 2 SB 1 FSI S2 1 0.98 32.066 8 | 3 NB 1 FSI N3 2 -0.58 14.000 9 | 4 OB 1 FSI O4 3 -0.48 15.999 10 | 5 OB 1 FSI O5 4 -0.48 15.999 11 | 6 SB 1 FSI S6 5 0.98 32.066 12 | 7 OB 1 FSI O7 6 -0.48 15.999 13 | 8 OB 1 FSI O6 7 -0.48 15.999 14 | 9 FB 1 FSI F7 8 -0.13 18.998 15 | 16 | [ pairs ] 17 | 1 6 1 18 | 2 7 1 19 | 2 8 1 20 | 2 9 1 21 | 4 6 1 22 | 5 6 1 23 | 24 | [ bonds ] 25 | 1 2 1 26 | 2 3 1 27 | 2 4 1 28 | 2 5 1 29 | 3 6 1 30 | 6 7 1 31 | 6 8 1 32 | 6 9 1 33 | 34 | [ angles ] 35 | ; ai aj ak funct c0 c1 c2 c3 36 | 1 2 4 1 37 | 1 2 5 1 38 | 9 6 8 1 39 | 9 6 7 1 40 | 1 2 3 1 41 | 9 6 3 1 42 | 4 2 5 1 43 | 7 6 8 1 44 | 4 2 3 1 45 | 5 2 3 1 46 | 7 6 3 1 47 | 8 6 3 1 48 | 2 3 6 1 49 | 50 | [ dihedrals ] 51 | 1 2 3 6 5 52 | 9 6 3 2 5 53 | 4 2 3 6 5 54 | 5 2 3 6 5 55 | 7 6 3 2 5 56 | 8 6 3 2 5 57 | 58 | -------------------------------------------------------------------------------- /topologies/py14fsi/pyr.gro: -------------------------------------------------------------------------------- 1 | PYR+ 2 | 30 3 | 1PYR N1 1 0.000 0.000 0.000 4 | 1PYR C2 2 0.000 0.000 0.147 5 | 1PYR C3 3 0.139 0.000 -0.049 6 | 1PYR C4 4 0.144 0.000 0.198 7 | 1PYR C5 5 0.235 0.000 0.070 8 | 1PYR C6 6 -0.069 -0.120 -0.049 9 | 1PYR C7 7 -0.069 0.120 -0.049 10 | 1PYR H8 8 -0.051 -0.089 0.183 11 | 1PYR H9 9 -0.051 0.089 0.183 12 | 1PYR H10 10 0.156 -0.089 -0.110 13 | 1PYR H11 11 0.156 0.089 -0.110 14 | 1PYR H12 12 0.163 -0.088 0.259 15 | 1PYR H13 13 0.163 0.088 0.259 16 | 1PYR H14 14 0.299 -0.088 0.068 17 | 1PYR H15 15 0.299 0.088 0.068 18 | 1PYR H16 16 -0.172 -0.120 -0.013 19 | 1PYR H17 17 -0.069 -0.120 -0.158 20 | 1PYR H18 18 -0.018 -0.209 -0.013 21 | 1PYR H19 19 -0.069 0.120 -0.158 22 | 1PYR H20 20 -0.172 0.120 -0.013 23 | 1PYR C21 21 0.003 0.245 0.002 24 | 1PYR H22 22 0.105 0.245 -0.035 25 | 1PYR H23 23 0.003 0.245 0.111 26 | 1PYR C24 24 -0.069 0.370 -0.049 27 | 1PYR H25 25 -0.172 0.370 -0.013 28 | 1PYR H26 26 -0.069 0.370 -0.158 29 | 1PYR C27 27 0.003 0.495 0.002 30 | 1PYR H28 28 0.105 0.495 -0.035 31 | 1PYR H29 29 0.003 0.495 0.111 32 | 1PYR H30 30 -0.049 0.584 -0.035 33 | 3.39953 3.39953 3.39953 34 | -------------------------------------------------------------------------------- /topologies/py14fsi/pyr.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | PYR 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 NT 1 PYR N1 0 0.096 14.0067 7 | 2 CT 1 PYR C2 1 -0.136 12.011 8 | 3 CT 1 PYR C3 2 -0.136 12.011 9 | 4 CT 1 PYR C4 3 0.008 12.011 10 | 5 CT 1 PYR C5 4 0.008 12.011 11 | 6 CT 1 PYR C6 5 -0.136 12.011 12 | 7 CT 1 PYR C7 6 -0.136 12.011 13 | 8 HC 1 PYR H8 7 0.104 1.008 14 | 9 HC 1 PYR H9 8 0.104 1.008 15 | 10 HC 1 PYR H10 9 0.104 1.008 16 | 11 HC 1 PYR H11 10 0.104 1.008 17 | 12 HC 1 PYR H12 11 0.048 1.008 18 | 13 HC 1 PYR H13 12 0.048 1.008 19 | 14 HC 1 PYR H14 13 0.048 1.008 20 | 15 HC 1 PYR H15 14 0.048 1.008 21 | 16 HC 1 PYR H16 15 0.104 1.008 22 | 17 HC 1 PYR H17 16 0.104 1.008 23 | 18 HC 1 PYR H18 17 0.104 1.008 24 | 19 HC 1 PYR H19 18 0.104 1.008 25 | 20 HC 1 PYR H20 19 0.104 1.008 26 | 21 CT 1 PYR C21 20 0.008 12.011 27 | 22 HC 1 PYR H22 21 0.048 1.008 28 | 23 HC 1 PYR H23 22 0.048 1.008 29 | 24 CT 1 PYR C24 23 -0.12 12.011 30 | 25 HC 1 PYR H25 24 0.06 1.008 31 | 26 HC 1 PYR H26 25 0.06 1.008 32 | 27 CT 1 PYR C27 26 -0.18 12.011 33 | 28 HC 1 PYR H28 27 0.06 1.008 34 | 29 HC 1 PYR H29 28 0.06 1.008 35 | 30 HC 1 PYR H30 29 0.06 1.008 36 | 37 | [ pairs ] 38 | 1 4 1 39 | 1 14 1 40 | 1 15 1 41 | 1 12 1 42 | 1 13 1 43 | 1 24 1 44 | 1 22 1 45 | 1 23 1 46 | 47 | 2 3 1 48 | 2 14 1 49 | 2 15 1 50 | 2 10 1 51 | 2 11 1 52 | 2 16 1 53 | 2 17 1 54 | 2 18 1 55 | 2 19 1 56 | 2 20 1 57 | 2 21 1 58 | 59 | 3 16 1 60 | 3 17 1 61 | 3 18 1 62 | 3 12 1 63 | 3 13 1 64 | 3 8 1 65 | 3 9 1 66 | 3 21 1 67 | 3 19 1 68 | 3 20 1 69 | 70 | 4 10 1 71 | 4 11 1 72 | 4 6 1 73 | 4 7 1 74 | 75 | 5 8 1 76 | 5 9 1 77 | 5 6 1 78 | 5 7 1 79 | 5 8 1 80 | 5 9 1 81 | 82 | 6 10 1 83 | 6 11 1 84 | 6 21 1 85 | 6 8 1 86 | 6 9 1 87 | 6 20 1 88 | 6 19 1 89 | 90 | 7 17 1 91 | 7 18 1 92 | 7 16 1 93 | 7 10 1 94 | 7 11 1 95 | 7 8 1 96 | 7 9 1 97 | 7 25 1 98 | 7 26 1 99 | 7 27 1 100 | 101 | 8 12 1 102 | 8 13 1 103 | 104 | 9 12 1 105 | 9 13 1 106 | 107 | 10 14 1 108 | 10 15 1 109 | 110 | 11 14 1 111 | 11 15 1 112 | 113 | 12 14 1 114 | 12 15 1 115 | 116 | 13 14 1 117 | 13 15 1 118 | 119 | 19 22 1 120 | 19 23 1 121 | 19 24 1 122 | 123 | 20 22 1 124 | 20 23 1 125 | 20 24 1 126 | 127 | 21 28 1 128 | 21 29 1 129 | 21 30 1 130 | 131 | 22 25 1 132 | 22 26 1 133 | 22 27 1 134 | 135 | 23 25 1 136 | 23 26 1 137 | 23 27 1 138 | 139 | 25 28 1 140 | 25 29 1 141 | 25 30 1 142 | 143 | 26 28 1 144 | 26 29 1 145 | 26 30 1 146 | 147 | 148 | [ bonds ] 149 | 1 2 1 150 | 1 3 1 151 | 1 6 1 152 | 1 7 1 153 | 2 4 1 154 | 2 8 1 155 | 2 9 1 156 | 4 12 1 157 | 4 13 1 158 | 4 5 1 159 | 5 14 1 160 | 5 15 1 161 | 5 3 1 162 | 3 10 1 163 | 3 11 1 164 | 6 16 1 165 | 6 17 1 166 | 6 18 1 167 | 7 19 1 168 | 7 20 1 169 | 7 21 1 170 | 21 22 1 171 | 21 23 1 172 | 21 24 1 173 | 24 25 1 174 | 24 26 1 175 | 24 27 1 176 | 27 28 1 177 | 27 29 1 178 | 27 30 1 179 | 180 | [ angles ] 181 | ; ai aj ak funct c0 c1 c2 c3 182 | 2 4 5 1 183 | 3 5 4 1 184 | 7 21 24 1 185 | 21 24 27 1 186 | 187 | 2 4 12 1 188 | 2 4 13 1 189 | 4 2 8 1 190 | 4 2 9 1 191 | 4 5 14 1 192 | 4 5 15 1 193 | 5 4 12 1 194 | 5 4 13 1 195 | 5 3 10 1 196 | 5 3 11 1 197 | 3 5 14 1 198 | 3 5 14 1 199 | 7 21 22 1 200 | 7 21 23 1 201 | 21 7 19 1 202 | 21 7 20 1 203 | 21 24 25 1 204 | 21 24 26 1 205 | 24 21 22 1 206 | 24 21 23 1 207 | 24 27 28 1 208 | 24 27 29 1 209 | 24 27 30 1 210 | 27 24 25 1 211 | 27 24 26 1 212 | 213 | 8 2 9 1 214 | 12 4 13 1 215 | 14 5 15 1 216 | 10 3 11 1 217 | 16 6 17 1 218 | 16 6 18 1 219 | 17 6 18 1 220 | 19 7 20 1 221 | 22 21 23 1 222 | 25 24 26 1 223 | 28 27 29 1 224 | 28 27 30 1 225 | 29 27 30 1 226 | 227 | 1 3 5 1 228 | 1 2 4 1 229 | 1 7 21 1 230 | 231 | 2 1 3 1 232 | 6 1 7 1 233 | 3 1 7 1 234 | 2 1 6 1 235 | 2 1 7 1 236 | 3 1 6 1 237 | 238 | 10 3 1 1 239 | 11 3 1 1 240 | 8 2 1 1 241 | 9 2 1 1 242 | 16 6 1 1 243 | 17 6 1 1 244 | 18 6 1 1 245 | 19 7 1 1 246 | 20 7 1 1 247 | 248 | 249 | [ dihedrals ] 250 | ;HC-CT-CT-HC 251 | 9 2 4 12 5 252 | 9 2 4 13 5 253 | 8 2 4 12 5 254 | 8 2 4 13 5 255 | 12 4 5 14 5 256 | 12 4 5 15 5 257 | 13 4 5 14 5 258 | 13 4 5 15 5 259 | 25 24 27 28 5 260 | 25 24 27 29 5 261 | 25 24 27 30 5 262 | 26 24 27 28 5 263 | 26 24 27 29 5 264 | 26 24 27 30 5 265 | 14 5 3 10 5 266 | 14 5 3 11 5 267 | 15 5 3 10 5 268 | 15 5 3 11 5 269 | 19 7 21 23 5 270 | 19 7 21 22 5 271 | 20 7 21 23 5 272 | 20 7 21 22 5 273 | 22 21 24 25 5 274 | 22 21 24 26 5 275 | 23 21 24 25 5 276 | 23 21 24 26 5 277 | ;CT-CT-CT-HC 278 | 2 4 5 14 5 279 | 2 4 5 15 5 280 | 4 5 3 10 5 281 | 4 5 3 11 5 282 | 3 5 4 12 5 283 | 3 5 4 13 5 284 | 5 4 2 8 5 285 | 5 4 2 9 5 286 | 7 21 24 25 5 287 | 7 21 24 26 5 288 | 21 24 27 28 5 289 | 21 24 27 29 5 290 | 21 24 27 30 5 291 | 27 24 21 22 5 292 | 27 24 21 23 5 293 | 24 21 7 19 5 294 | 24 21 7 20 5 295 | ;CT-CT-CT-CT 296 | 2 4 5 3 5 297 | 7 21 24 27 5 298 | ;HC-CT-CT-NT 299 | 14 5 3 1 5 300 | 15 5 3 1 5 301 | 12 4 2 1 5 302 | 13 4 2 1 5 303 | 22 21 7 1 5 304 | 23 21 7 1 5 305 | ;CT-CT-CT-NT 306 | 5 4 2 1 5 307 | 4 5 3 1 5 308 | 24 21 7 1 5 309 | ;CT-NT-CT-CT 310 | 2 1 3 5 5 311 | 2 1 7 21 5 312 | 3 1 2 4 5 313 | 3 1 7 21 5 314 | 7 1 3 5 5 315 | 7 1 2 4 5 316 | 6 1 2 4 5 317 | 6 1 3 5 5 318 | 6 1 7 21 5 319 | ;HC-CT-NT-CT 320 | 8 2 1 6 5 321 | 9 2 1 6 5 322 | 8 2 1 3 5 323 | 9 2 1 3 5 324 | 8 2 1 7 5 325 | 9 2 1 7 5 326 | 10 3 1 2 5 327 | 11 3 1 2 5 328 | 10 3 1 6 5 329 | 11 3 1 6 5 330 | 10 3 1 7 5 331 | 11 3 1 7 5 332 | 19 7 1 2 5 333 | 20 7 1 2 5 334 | 19 7 1 3 5 335 | 20 7 1 3 5 336 | 19 7 1 6 5 337 | 20 7 1 6 5 338 | 16 6 1 2 5 339 | 17 6 1 2 5 340 | 18 6 1 2 5 341 | 16 6 1 3 5 342 | 17 6 1 3 5 343 | 18 6 1 3 5 344 | 16 6 1 7 5 345 | 17 6 1 7 5 346 | 18 6 1 7 5 347 | 348 | -------------------------------------------------------------------------------- /topologies/py14fsi/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "pyr.itp" 3 | #include "fsi.itp" 4 | 5 | [system] 6 | PYR FSI 7 | 8 | 9 | [molecules] 10 | PYR 125 11 | FSI 125 12 | -------------------------------------------------------------------------------- /topologies/py14tf/Tf.gro: -------------------------------------------------------------------------------- 1 | TF- 2 | 8 3 | 1TF C1 1 0.036 -0.047 -0.261 4 | 1TF F2 2 -0.047 -0.143 -0.313 5 | 1TF F3 3 0.116 0.003 -0.360 6 | 1TF F4 4 0.116 -0.107 -0.165 7 | 1TF S5 5 -0.070 0.096 -0.177 8 | 1TF O6 6 0.045 0.197 -0.116 9 | 1TF O7 7 -0.164 0.154 -0.297 10 | 1TF O8 8 -0.147 0.013 -0.055 11 | 3.39953 3.39953 3.39953 12 | -------------------------------------------------------------------------------- /topologies/py14tf/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ;pyrrolidinium JPCB108(2004)16893 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NT 7 14.007 0.12 A 0.325 0.71128 10 | ;TF 11 | FB 9 18.998 -0.49 A 0.312 0.2552 12 | SB 16 32.064 1.02 A 0.355 1.04600 13 | OB 8 15.9994 -0.63 A 0.296 0.87864 14 | CB 6 12.011 0.35 A 0.350 0.27614 15 | 16 | [ bondtypes ] 17 | ; this is for pyrrolidinium 18 | HC CT 1 0.1090 -284500 ; - 19 | CT CT 1 0.1529 224200 ; 20 | NT CT 1 0.1471 307100.0 21 | ;TF 22 | CB FB 1 0.1323 369800 23 | CB SB 1 0.1818 195000 24 | SB OB 1 0.1437 533100 25 | 26 | [ angletypes ] 27 | CT CT CT 1 112.7 488.3 28 | CT CT HC 1 110.7 313.8 29 | HC CT HC 1 107.8 276.1 30 | NT CT CT 1 109.5 669.4 31 | CT NT CT 1 109.5 418.4 32 | HC CT NT 1 109.5 209.2 33 | ;TF 34 | FB CB FB 1 107.1 781.0 35 | FB CB SB 1 111.7 694.0 36 | OB SB OB 1 118.5 969.0 37 | CB SB OB 1 102.6 870.0 38 | 39 | [ dihedraltypes ] 40 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 41 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 42 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 43 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 44 | ;pyrrolidilium 45 | HC CT CT NT 5 -4.2384 -2.9665 1.9790 0.0000 46 | CT CT CT NT 5 10.0081 -2.8200 2.3012 0.0000 47 | CT NT CT CT 5 1.7405 -0.5356 2.9079 0.0000 48 | HC CT NT CT 5 0.0000 0.0000 2.3430 0.0000 49 | ;triflate JPCB108(2004)16893 50 | OB SB CB FB 5 0.0000 0.0000 1.4510 0.0000 51 | -------------------------------------------------------------------------------- /topologies/py14tf/pyr.gro: -------------------------------------------------------------------------------- 1 | PYR+ 2 | 30 3 | 1PYR N1 1 0.000 0.000 0.000 4 | 1PYR C2 2 0.000 0.000 0.147 5 | 1PYR C3 3 0.139 0.000 -0.049 6 | 1PYR C4 4 0.144 0.000 0.198 7 | 1PYR C5 5 0.235 0.000 0.070 8 | 1PYR C6 6 -0.069 -0.120 -0.049 9 | 1PYR C7 7 -0.069 0.120 -0.049 10 | 1PYR H8 8 -0.051 -0.089 0.183 11 | 1PYR H9 9 -0.051 0.089 0.183 12 | 1PYR H10 10 0.156 -0.089 -0.110 13 | 1PYR H11 11 0.156 0.089 -0.110 14 | 1PYR H12 12 0.163 -0.088 0.259 15 | 1PYR H13 13 0.163 0.088 0.259 16 | 1PYR H14 14 0.299 -0.088 0.068 17 | 1PYR H15 15 0.299 0.088 0.068 18 | 1PYR H16 16 -0.172 -0.120 -0.013 19 | 1PYR H17 17 -0.069 -0.120 -0.158 20 | 1PYR H18 18 -0.018 -0.209 -0.013 21 | 1PYR H19 19 -0.069 0.120 -0.158 22 | 1PYR H20 20 -0.172 0.120 -0.013 23 | 1PYR C21 21 0.003 0.245 0.002 24 | 1PYR H22 22 0.105 0.245 -0.035 25 | 1PYR H23 23 0.003 0.245 0.111 26 | 1PYR C24 24 -0.069 0.370 -0.049 27 | 1PYR H25 25 -0.172 0.370 -0.013 28 | 1PYR H26 26 -0.069 0.370 -0.158 29 | 1PYR C27 27 0.003 0.495 0.002 30 | 1PYR H28 28 0.105 0.495 -0.035 31 | 1PYR H29 29 0.003 0.495 0.111 32 | 1PYR H30 30 -0.049 0.584 -0.035 33 | 3.39953 3.39953 3.39953 34 | -------------------------------------------------------------------------------- /topologies/py14tf/tf.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | TF 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 CB 1 TF C1 1 0.2520 12.011 7 | 2 FB 1 TF F2 2 -0.1152 18.998 8 | 3 FB 1 TF F3 3 -0.1152 18.998 9 | 4 FB 1 TF F4 4 -0.1152 18.998 10 | 5 SB 1 TF S5 5 0.7344 32.066 11 | 6 OB 1 TF O6 6 -0.4536 15.999 12 | 7 OB 1 TF O7 7 -0.4536 15.999 13 | 8 OB 1 TF O8 8 -0.4536 15.999 14 | 15 | [ pairs ] 16 | 3 8 1 17 | 3 6 1 18 | 3 7 1 19 | 4 7 1 20 | 4 6 1 21 | 2 7 1 22 | 2 6 1 23 | 2 8 1 24 | 25 | [ bonds ] 26 | 1 2 1 27 | 1 3 1 28 | 1 4 1 29 | 1 5 1 30 | 5 6 1 31 | 5 7 1 32 | 5 8 1 33 | 34 | [ angles ] 35 | 2 1 3 1 36 | 2 1 4 1 37 | 3 1 4 1 38 | 2 1 5 1 39 | 3 1 5 1 40 | 4 1 5 1 41 | 6 5 7 1 42 | 6 5 8 1 43 | 7 5 8 1 44 | 1 5 6 1 45 | 1 5 7 1 46 | 1 5 8 1 47 | 48 | [ dihedrals ] 49 | 6 5 1 2 5 50 | 6 5 1 3 5 51 | 6 5 1 4 5 52 | 7 5 1 2 5 53 | 7 5 1 3 5 54 | 7 5 1 4 5 55 | 8 5 1 2 5 56 | 8 5 1 3 5 57 | 8 5 1 4 5 58 | 59 | -------------------------------------------------------------------------------- /topologies/py14tf/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "pyr.itp" 3 | #include "tf.itp" 4 | 5 | [system] 6 | PYR TF 7 | 8 | 9 | [molecules] 10 | PYR 125 11 | TF 125 12 | -------------------------------------------------------------------------------- /topologies/py14tfsi/ff.itp: -------------------------------------------------------------------------------- 1 | [ defaults ] 2 | ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 3 | 1 3 yes 0.5 0.5 4 | 5 | [ atomtypes ] 6 | ;pyrrolidinium JPCB108(2004)16893 7 | CT 6 12.011 -0.18 A 0.350 0.27614 8 | HC 1 1.008 0.06 A 0.250 0.12552 9 | NT 7 14.007 0.12 A 0.325 0.71128 10 | ; TFSI 11 | SO 16 32.064 1.02 A 0.355 1.04600 12 | OS 8 15.9994 -0.53 A 0.296 0.87864 13 | FC 9 18.9984 -0.16 A 0.295 0.22175 14 | CF 6 12.011 0.35 A 0.350 0.27614 15 | NI 7 14.0027 -0.66 A 0.325 0.71128 16 | 17 | [ bondtypes ] 18 | ; this is for pyrrolidinium 19 | HC CT 1 0.1090 -284500 ; - 20 | CT CT 1 0.1529 224200 ; 21 | NT CT 1 0.1471 307100.0 22 | ; TFSI 23 | CF FC 1 0.1323 369700 24 | CF SO 1 0.1818 197000 25 | SO OS 1 0.1442 533100 26 | NI SO 1 0.1570 311300 27 | 28 | [ angletypes ] 29 | CT CT CT 1 112.7 488.3 30 | CT CT HC 1 110.7 313.8 31 | HC CT HC 1 107.8 276.1 32 | NT CT CT 1 109.5 669.4 33 | CT NT CT 1 109.5 418.4 34 | HC CT NT 1 109.5 209.2 35 | ; TFSI 36 | OS SO OS 1 118.5 969 37 | OS SO NI 1 113.6 789 38 | CF SO NI 1 100.2 816 39 | SO NI SO 1 125.6 671 40 | FC CF FC 1 107.1 781 41 | FC CF SO 1 111.7 694 42 | CF SO OS 1 102.6 870 43 | 44 | [ dihedraltypes ] 45 | ; alkanes OPLS-AA JACS118:11225(1996); JPC100:18010(1996) 46 | HC CT CT HC 5 0.0000 0.0000 1.3305 0.0000 47 | CT CT CT HC 5 0.0000 0.0000 1.5313 0.0000 48 | CT CT CT CT 5 7.2800 -0.6569 1.1673 0.0000 49 | ;pyrrolidilium 50 | HC CT CT NT 5 -4.2384 -2.9665 1.9790 0.0000 51 | CT CT CT NT 5 10.0081 -2.8200 2.3012 0.0000 52 | CT NT CT CT 5 1.7405 -0.5356 2.9079 0.0000 53 | HC CT NT CT 5 0.0000 0.0000 2.3430 0.0000 54 | ; TFSI 55 | OS SO CF FC 5 0.0000 0.0000 1.4510 0.0000 56 | NI SO CF FC 5 0.0000 0.0000 1.3220 0.0000 57 | OS SO NI SO 5 0.0000 0.0000 -0.0150 0.0000 58 | SO NI SO CF 5 32.7730 -10.4200 -3.1950 0.0000 59 | -------------------------------------------------------------------------------- /topologies/py14tfsi/pyr.gro: -------------------------------------------------------------------------------- 1 | PYR+ 2 | 30 3 | 1PYR N1 1 0.000 0.000 0.000 4 | 1PYR C2 2 0.000 0.000 0.147 5 | 1PYR C3 3 0.139 0.000 -0.049 6 | 1PYR C4 4 0.144 0.000 0.198 7 | 1PYR C5 5 0.235 0.000 0.070 8 | 1PYR C6 6 -0.069 -0.120 -0.049 9 | 1PYR C7 7 -0.069 0.120 -0.049 10 | 1PYR H8 8 -0.051 -0.089 0.183 11 | 1PYR H9 9 -0.051 0.089 0.183 12 | 1PYR H10 10 0.156 -0.089 -0.110 13 | 1PYR H11 11 0.156 0.089 -0.110 14 | 1PYR H12 12 0.163 -0.088 0.259 15 | 1PYR H13 13 0.163 0.088 0.259 16 | 1PYR H14 14 0.299 -0.088 0.068 17 | 1PYR H15 15 0.299 0.088 0.068 18 | 1PYR H16 16 -0.172 -0.120 -0.013 19 | 1PYR H17 17 -0.069 -0.120 -0.158 20 | 1PYR H18 18 -0.018 -0.209 -0.013 21 | 1PYR H19 19 -0.069 0.120 -0.158 22 | 1PYR H20 20 -0.172 0.120 -0.013 23 | 1PYR C21 21 0.003 0.245 0.002 24 | 1PYR H22 22 0.105 0.245 -0.035 25 | 1PYR H23 23 0.003 0.245 0.111 26 | 1PYR C24 24 -0.069 0.370 -0.049 27 | 1PYR H25 25 -0.172 0.370 -0.013 28 | 1PYR H26 26 -0.069 0.370 -0.158 29 | 1PYR C27 27 0.003 0.495 0.002 30 | 1PYR H28 28 0.105 0.495 -0.035 31 | 1PYR H29 29 0.003 0.495 0.111 32 | 1PYR H30 30 -0.049 0.584 -0.035 33 | 3.39953 3.39953 3.39953 34 | -------------------------------------------------------------------------------- /topologies/py14tfsi/pyr.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | PYR 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 NT 1 PYR N1 0 0.096 14.0067 7 | 2 CT 1 PYR C2 1 -0.136 12.011 8 | 3 CT 1 PYR C3 2 -0.136 12.011 9 | 4 CT 1 PYR C4 3 0.008 12.011 10 | 5 CT 1 PYR C5 4 0.008 12.011 11 | 6 CT 1 PYR C6 5 -0.136 12.011 12 | 7 CT 1 PYR C7 6 -0.136 12.011 13 | 8 HC 1 PYR H8 7 0.104 1.008 14 | 9 HC 1 PYR H9 8 0.104 1.008 15 | 10 HC 1 PYR H10 9 0.104 1.008 16 | 11 HC 1 PYR H11 10 0.104 1.008 17 | 12 HC 1 PYR H12 11 0.048 1.008 18 | 13 HC 1 PYR H13 12 0.048 1.008 19 | 14 HC 1 PYR H14 13 0.048 1.008 20 | 15 HC 1 PYR H15 14 0.048 1.008 21 | 16 HC 1 PYR H16 15 0.104 1.008 22 | 17 HC 1 PYR H17 16 0.104 1.008 23 | 18 HC 1 PYR H18 17 0.104 1.008 24 | 19 HC 1 PYR H19 18 0.104 1.008 25 | 20 HC 1 PYR H20 19 0.104 1.008 26 | 21 CT 1 PYR C21 20 0.008 12.011 27 | 22 HC 1 PYR H22 21 0.048 1.008 28 | 23 HC 1 PYR H23 22 0.048 1.008 29 | 24 CT 1 PYR C24 23 -0.12 12.011 30 | 25 HC 1 PYR H25 24 0.06 1.008 31 | 26 HC 1 PYR H26 25 0.06 1.008 32 | 27 CT 1 PYR C27 26 -0.18 12.011 33 | 28 HC 1 PYR H28 27 0.06 1.008 34 | 29 HC 1 PYR H29 28 0.06 1.008 35 | 30 HC 1 PYR H30 29 0.06 1.008 36 | 37 | [ pairs ] 38 | 1 4 1 39 | 1 14 1 40 | 1 15 1 41 | 1 12 1 42 | 1 13 1 43 | 1 24 1 44 | 1 22 1 45 | 1 23 1 46 | 47 | 2 3 1 48 | 2 14 1 49 | 2 15 1 50 | 2 10 1 51 | 2 11 1 52 | 2 16 1 53 | 2 17 1 54 | 2 18 1 55 | 2 19 1 56 | 2 20 1 57 | 2 21 1 58 | 59 | 3 16 1 60 | 3 17 1 61 | 3 18 1 62 | 3 12 1 63 | 3 13 1 64 | 3 8 1 65 | 3 9 1 66 | 3 21 1 67 | 3 19 1 68 | 3 20 1 69 | 70 | 4 10 1 71 | 4 11 1 72 | 4 6 1 73 | 4 7 1 74 | 75 | 5 8 1 76 | 5 9 1 77 | 5 6 1 78 | 5 7 1 79 | 5 8 1 80 | 5 9 1 81 | 82 | 6 10 1 83 | 6 11 1 84 | 6 21 1 85 | 6 8 1 86 | 6 9 1 87 | 6 20 1 88 | 6 19 1 89 | 90 | 7 17 1 91 | 7 18 1 92 | 7 16 1 93 | 7 10 1 94 | 7 11 1 95 | 7 8 1 96 | 7 9 1 97 | 7 25 1 98 | 7 26 1 99 | 7 27 1 100 | 101 | 8 12 1 102 | 8 13 1 103 | 104 | 9 12 1 105 | 9 13 1 106 | 107 | 10 14 1 108 | 10 15 1 109 | 110 | 11 14 1 111 | 11 15 1 112 | 113 | 12 14 1 114 | 12 15 1 115 | 116 | 13 14 1 117 | 13 15 1 118 | 119 | 19 22 1 120 | 19 23 1 121 | 19 24 1 122 | 123 | 20 22 1 124 | 20 23 1 125 | 20 24 1 126 | 127 | 21 28 1 128 | 21 29 1 129 | 21 30 1 130 | 131 | 22 25 1 132 | 22 26 1 133 | 22 27 1 134 | 135 | 23 25 1 136 | 23 26 1 137 | 23 27 1 138 | 139 | 25 28 1 140 | 25 29 1 141 | 25 30 1 142 | 143 | 26 28 1 144 | 26 29 1 145 | 26 30 1 146 | 147 | [ bonds ] 148 | 1 2 1 149 | 1 3 1 150 | 1 6 1 151 | 1 7 1 152 | 2 4 1 153 | 2 8 1 154 | 2 9 1 155 | 4 12 1 156 | 4 13 1 157 | 4 5 1 158 | 5 14 1 159 | 5 15 1 160 | 5 3 1 161 | 3 10 1 162 | 3 11 1 163 | 6 16 1 164 | 6 17 1 165 | 6 18 1 166 | 7 19 1 167 | 7 20 1 168 | 7 21 1 169 | 21 22 1 170 | 21 23 1 171 | 21 24 1 172 | 24 25 1 173 | 24 26 1 174 | 24 27 1 175 | 27 28 1 176 | 27 29 1 177 | 27 30 1 178 | 179 | [ angles ] 180 | ; ai aj ak funct c0 c1 c2 c3 181 | 2 4 5 1 182 | 3 5 4 1 183 | 7 21 24 1 184 | 21 24 27 1 185 | 186 | 2 4 12 1 187 | 2 4 13 1 188 | 4 2 8 1 189 | 4 2 9 1 190 | 4 5 14 1 191 | 4 5 15 1 192 | 5 4 12 1 193 | 5 4 13 1 194 | 5 3 10 1 195 | 5 3 11 1 196 | 3 5 14 1 197 | 3 5 14 1 198 | 7 21 22 1 199 | 7 21 23 1 200 | 21 7 19 1 201 | 21 7 20 1 202 | 21 24 25 1 203 | 21 24 26 1 204 | 24 21 22 1 205 | 24 21 23 1 206 | 24 27 28 1 207 | 24 27 29 1 208 | 24 27 30 1 209 | 27 24 25 1 210 | 27 24 26 1 211 | 212 | 8 2 9 1 213 | 12 4 13 1 214 | 14 5 15 1 215 | 10 3 11 1 216 | 16 6 17 1 217 | 16 6 18 1 218 | 17 6 18 1 219 | 19 7 20 1 220 | 22 21 23 1 221 | 25 24 26 1 222 | 28 27 29 1 223 | 28 27 30 1 224 | 29 27 30 1 225 | 226 | 1 3 5 1 227 | 1 2 4 1 228 | 1 7 21 1 229 | 230 | 2 1 3 1 231 | 6 1 7 1 232 | 3 1 7 1 233 | 2 1 6 1 234 | 2 1 7 1 235 | 3 1 6 1 236 | 237 | 10 3 1 1 238 | 11 3 1 1 239 | 8 2 1 1 240 | 9 2 1 1 241 | 16 6 1 1 242 | 17 6 1 1 243 | 18 6 1 1 244 | 19 7 1 1 245 | 20 7 1 1 246 | 247 | 248 | [ dihedrals ] 249 | ;HC-CT-CT-HC 250 | 9 2 4 12 5 251 | 9 2 4 13 5 252 | 8 2 4 12 5 253 | 8 2 4 13 5 254 | 12 4 5 14 5 255 | 12 4 5 15 5 256 | 13 4 5 14 5 257 | 13 4 5 15 5 258 | 25 24 27 28 5 259 | 25 24 27 29 5 260 | 25 24 27 30 5 261 | 26 24 27 28 5 262 | 26 24 27 29 5 263 | 26 24 27 30 5 264 | 14 5 3 10 5 265 | 14 5 3 11 5 266 | 15 5 3 10 5 267 | 15 5 3 11 5 268 | 19 7 21 23 5 269 | 19 7 21 22 5 270 | 20 7 21 23 5 271 | 20 7 21 22 5 272 | 22 21 24 25 5 273 | 22 21 24 26 5 274 | 23 21 24 25 5 275 | 23 21 24 26 5 276 | ;CT-CT-CT-HC 277 | 2 4 5 14 5 278 | 2 4 5 15 5 279 | 4 5 3 10 5 280 | 4 5 3 11 5 281 | 3 5 4 12 5 282 | 3 5 4 13 5 283 | 5 4 2 8 5 284 | 5 4 2 9 5 285 | 7 21 24 25 5 286 | 7 21 24 26 5 287 | 21 24 27 28 5 288 | 21 24 27 29 5 289 | 21 24 27 30 5 290 | 27 24 21 22 5 291 | 27 24 21 23 5 292 | 24 21 7 19 5 293 | 24 21 7 20 5 294 | ;CT-CT-CT-CT 295 | 2 4 5 3 5 296 | 7 21 24 27 5 297 | ;HC-CT-CT-NT 298 | 14 5 3 1 5 299 | 15 5 3 1 5 300 | 12 4 2 1 5 301 | 13 4 2 1 5 302 | 22 21 7 1 5 303 | 23 21 7 1 5 304 | ;CT-CT-CT-NT 305 | 5 4 2 1 5 306 | 4 5 3 1 5 307 | 24 21 7 1 5 308 | ;CT-NT-CT-CT 309 | 2 1 3 5 5 310 | 2 1 7 21 5 311 | 3 1 2 4 5 312 | 3 1 7 21 5 313 | 7 1 3 5 5 314 | 7 1 2 4 5 315 | 6 1 2 4 5 316 | 6 1 3 5 5 317 | 6 1 7 21 5 318 | ;HC-CT-NT-CT 319 | 8 2 1 6 5 320 | 9 2 1 6 5 321 | 8 2 1 3 5 322 | 9 2 1 3 5 323 | 8 2 1 7 5 324 | 9 2 1 7 5 325 | 10 3 1 2 5 326 | 11 3 1 2 5 327 | 10 3 1 6 5 328 | 11 3 1 6 5 329 | 10 3 1 7 5 330 | 11 3 1 7 5 331 | 19 7 1 2 5 332 | 20 7 1 2 5 333 | 19 7 1 3 5 334 | 20 7 1 3 5 335 | 19 7 1 6 5 336 | 20 7 1 6 5 337 | 16 6 1 2 5 338 | 17 6 1 2 5 339 | 18 6 1 2 5 340 | 16 6 1 3 5 341 | 17 6 1 3 5 342 | 18 6 1 3 5 343 | 16 6 1 7 5 344 | 17 6 1 7 5 345 | 18 6 1 7 5 346 | -------------------------------------------------------------------------------- /topologies/py14tfsi/tfsi.gro: -------------------------------------------------------------------------------- 1 | TFSI- 2 | 15 3 | 1TFS NI 1 2.667 0.846 3.946 4 | 1TFS SO 2 2.821 0.885 3.943 5 | 1TFS SO 3 2.598 0.705 3.945 6 | 1TFS OS 4 2.454 0.707 3.927 7 | 1TFS OS 5 2.664 0.595 3.884 8 | 1TFS OS 6 2.913 0.790 3.997 9 | 1TFS OS 7 2.844 1.022 3.978 10 | 1TFS CF 8 2.612 0.657 4.122 11 | 1TFS CF 9 2.853 0.874 3.757 12 | 1TFS FC 10 2.540 0.542 4.132 13 | 1TFS FC 11 2.568 0.750 4.208 14 | 1TFS FC 12 2.739 0.624 4.161 15 | 1TFS FC 13 2.974 0.888 3.723 16 | 1TFS FC 14 2.797 0.978 3.704 17 | 1TFS FC 15 2.795 0.770 3.699 18 | 3.96432 3.96432 3.96432 19 | -------------------------------------------------------------------------------- /topologies/py14tfsi/tfsi.itp: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | TFS 3 3 | 4 | [ atoms ] 5 | ; nr type resnr residue atom cgnr charge mass 6 | 1 NI 1 TFS NI 1 -0.4 14.0067 7 | 2 SO 1 TFS SO 2 0.6 32.06 8 | 3 SO 1 TFS SO 3 0.6 32.06 9 | 4 OS 1 TFS OS 4 -0.4 15.999 10 | 5 OS 1 TFS OS 5 -0.4 15.999 11 | 6 OS 1 TFS OS 6 -0.4 15.999 12 | 7 OS 1 TFS OS 7 -0.4 15.999 13 | 8 CF 1 TFS CF 8 0.3 12.011 14 | 9 CF 1 TFS CF 9 0.3 12.011 15 | 10 FC 1 TFS FC 10 -0.1 18.9984 16 | 11 FC 1 TFS FC 11 -0.1 18.9984 17 | 12 FC 1 TFS FC 12 -0.1 18.9984 18 | 13 FC 1 TFS FC 13 -0.1 18.9984 19 | 14 FC 1 TFS FC 14 -0.1 18.9984 20 | 15 FC 1 TFS FC 15 -0.1 18.9984 21 | 22 | [ pairs ] 23 | 2 4 1 24 | 2 5 1 25 | 3 6 1 26 | 3 7 1 27 | 10 4 1 28 | 11 4 1 29 | 12 4 1 30 | 10 5 1 31 | 11 5 1 32 | 12 5 1 33 | 1 10 1 34 | 1 11 1 35 | 1 12 1 36 | 37 | 8 2 1 38 | 9 3 1 39 | 40 | 13 6 1 41 | 14 6 1 42 | 15 6 1 43 | 13 7 1 44 | 14 7 1 45 | 15 7 1 46 | 13 1 1 47 | 14 1 1 48 | 15 1 1 49 | 50 | [ bonds ] 51 | 1 2 1 52 | 1 3 1 53 | 2 6 1 54 | 2 7 1 55 | 2 9 1 56 | 3 8 1 57 | 3 4 1 58 | 3 5 1 59 | 8 10 1 60 | 8 11 1 61 | 8 12 1 62 | 9 13 1 63 | 9 14 1 64 | 9 15 1 65 | 66 | [ pairs ] 67 | 2 4 1 68 | 2 5 1 69 | 3 6 1 70 | 3 7 1 71 | 10 4 1 72 | 11 4 1 73 | 12 4 1 74 | 10 5 1 75 | 11 5 1 76 | 12 5 1 77 | 1 10 1 78 | 1 11 1 79 | 1 12 1 80 | 81 | 8 2 1 82 | 9 3 1 83 | 84 | 13 6 1 85 | 14 6 1 86 | 15 6 1 87 | 13 7 1 88 | 14 7 1 89 | 15 7 1 90 | 13 1 1 91 | 14 1 1 92 | 15 1 1 93 | 94 | [ angles ] 95 | 13 9 14 1 96 | 13 9 15 1 97 | 14 9 15 1 98 | 13 9 2 1 99 | 14 9 2 1 100 | 15 9 2 1 101 | 9 2 6 1 102 | 9 2 7 1 103 | 9 2 1 1 104 | 2 1 3 1 105 | 6 2 1 1 106 | 7 2 1 1 107 | 1 3 4 1 108 | 1 3 5 1 109 | 1 3 8 1 110 | 4 3 8 1 111 | 5 3 8 1 112 | 3 8 10 1 113 | 3 8 11 1 114 | 3 8 12 1 115 | 10 8 11 1 116 | 10 8 12 1 117 | 11 8 12 1 118 | 6 2 7 1 119 | 4 3 5 1 120 | 121 | [ dihedrals ] 122 | 3 1 2 6 5 ; S-N-S-O 123 | 3 1 2 7 5 124 | 2 1 3 4 5 125 | 2 1 3 5 5 126 | 127 | 1 3 8 10 5 ; N-S-C-F 128 | 1 3 8 11 5 129 | 1 3 8 12 5 130 | 1 2 9 13 5 131 | 1 2 9 14 5 132 | 1 2 9 15 5 133 | 134 | 5 3 8 10 5 ; O-S-C-F 135 | 5 3 8 11 5 136 | 5 3 8 12 5 137 | 4 3 8 10 5 138 | 4 3 8 11 5 139 | 4 3 8 12 5 140 | 141 | 6 2 9 13 5 ; O-S-C-F 142 | 6 2 9 14 5 143 | 6 2 9 15 5 144 | 7 2 9 13 5 145 | 7 2 9 14 5 146 | 7 2 9 15 5 147 | 148 | 3 1 2 9 5 ; S-N-S-C 149 | 2 1 3 8 5 150 | -------------------------------------------------------------------------------- /topologies/py14tfsi/topol.top: -------------------------------------------------------------------------------- 1 | #include "ff.itp" 2 | #include "pyr.itp" 3 | #include "tfsi.itp" 4 | 5 | [system] 6 | PYR TFSI 7 | 8 | [molecules] 9 | PYR 125 10 | TFS 125 11 | 12 | -------------------------------------------------------------------------------- /tso.zmat: -------------------------------------------------------------------------------- 1 | tso- 2 | 3 | 1 CATS 4 | 2 CAOS 1 1.388 5 | 3 CAMS 2 1.388 1 120.0 6 | 4 CAOS 1 1.388 2 120.0 3 360.0 7 | 5 CAMS 4 1.388 1 120.0 2 0.0 8 | 6 CAPS 5 1.388 4 120.0 1 0.0 9 | 7 CTTS 1 1.512 2 120.0 3 180.0 10 | 8 SO 6 1.797 5 120.0 4 180.0 11 | 9 HATS 2 1.075 1 120.0 3 180.0 12 | 10 HATS 3 1.075 2 120.0 1 180.0 13 | 11 HATS 4 1.075 1 120.0 2 180.0 14 | 12 HATS 5 1.075 4 120.0 1 180.0 15 | 13 HTS 7 1.086 1 111.0 2 30.0 16 | 14 HTS 7 1.086 1 111.0 2 270.0 17 | 15 HTS 7 1.086 1 111.0 2 150.0 18 | 16 OS3 8 1.452 6 104.0 5 30.0 19 | 17 OS3 8 1.452 6 104.0 5 150.0 20 | 18 OS3 8 1.452 6 104.0 5 270.0 21 | 22 | connect 3 6 23 | 24 | il.ff 25 | --------------------------------------------------------------------------------