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revert to original pitorsion code

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This commit is contained in:
Steve Plimpton
2022-04-21 10:06:53 -06:00
parent 04ac4c4695
commit 501ef071c5
4 changed files with 109 additions and 110 deletions
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212
examples/amoeba/data.ubiquitin
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@ -26425,112 +26425,112 @@ BiTorsions
PiTorsions PiTorsions
1 1 2 4 3 20 24 21 1 1 2 4 3 20 21 24
2 1 21 23 22 37 41 38 2 1 21 23 22 37 38 41
3 1 27 29 28 30 36 35 3 1 27 29 28 30 35 36
4 1 38 40 39 56 60 57 4 1 38 40 39 56 57 60
5 1 57 59 58 76 80 77 5 1 57 59 58 76 77 80
6 2 62 65 63 64 71 66 6 2 62 65 63 64 66 71
7 2 62 64 63 65 72 67 7 2 62 64 63 65 67 72
8 2 63 71 64 66 73 68 8 2 63 71 64 66 68 73
9 2 63 72 65 67 74 68 9 2 63 72 65 67 68 74
10 2 64 73 66 68 75 67 10 2 64 73 66 68 67 75
11 2 65 74 67 68 75 66 11 2 65 74 67 68 66 75
12 1 77 79 78 92 96 93 12 1 77 79 78 92 93 96
13 1 93 95 94 114 118 115 13 1 93 95 94 114 115 118
14 1 115 117 116 128 132 129 14 1 115 117 116 128 129 132
15 1 129 131 130 147 151 148 15 1 129 131 130 147 148 151
16 1 148 150 149 161 165 162 16 1 148 150 149 161 162 165
17 1 162 164 163 168 172 169 17 1 162 164 163 168 169 172
18 1 169 171 170 190 194 191 18 1 169 171 170 190 191 194
19 1 191 193 192 204 208 205 19 1 191 193 192 204 205 208
20 1 205 207 206 223 227 224 20 1 205 207 206 223 224 227
21 1 224 226 225 237 241 238 21 1 224 226 225 237 238 241
22 1 238 240 239 256 260 257 22 1 238 240 239 256 257 260
23 1 257 259 258 271 275 272 23 1 257 259 258 271 272 275
24 1 272 274 273 287 291 288 24 1 272 274 273 287 288 291
25 3 288 290 289 302 309 303 25 3 288 290 289 302 303 309
26 1 303 305 304 316 320 317 26 1 303 305 304 316 317 320
27 1 317 319 318 327 331 328 27 1 317 319 318 327 328 331
28 1 328 330 329 339 343 340 28 1 328 330 329 339 340 343
29 1 340 342 341 353 357 354 29 1 340 342 341 353 354 357
30 1 354 356 355 372 376 373 30 1 354 356 355 372 373 376
31 1 373 375 374 387 391 388 31 1 373 375 374 387 388 391
32 1 388 390 389 401 405 402 32 1 388 390 389 401 402 405
33 1 393 395 394 396 400 399 33 1 393 395 394 396 399 400
34 1 402 404 403 417 421 418 34 1 402 404 403 417 418 421
35 1 418 420 419 439 443 440 35 1 418 420 419 439 440 443
36 1 440 442 441 449 453 450 36 1 440 442 441 449 450 453
37 1 450 452 451 471 475 472 37 1 450 452 451 471 472 475
38 1 472 474 473 490 494 491 38 1 472 474 473 490 491 494
39 1 491 493 492 507 511 508 39 1 491 493 492 507 508 511
40 1 497 499 498 500 506 505 40 1 497 499 498 500 505 506
41 1 508 510 509 519 523 520 41 1 508 510 509 519 520 523
42 1 520 522 521 541 545 542 42 1 520 522 521 541 542 545
43 1 542 544 543 556 560 557 43 1 542 544 543 556 557 560
44 1 557 559 558 563 567 564 44 1 557 559 558 563 564 567
45 3 564 566 565 582 589 583 45 3 564 566 565 582 583 589
46 3 583 585 584 596 603 597 46 3 583 585 584 596 597 603
47 1 597 599 598 610 614 611 47 1 597 599 598 610 611 614
48 1 611 613 612 622 626 623 48 1 611 613 612 622 623 626
49 1 623 625 624 639 643 640 49 1 623 625 624 639 640 643
50 1 629 631 630 632 638 637 50 1 629 631 630 632 637 638
51 1 640 642 641 656 660 657 51 1 640 642 641 656 657 660
52 1 646 648 647 649 655 654 52 1 646 648 647 649 654 655
53 1 657 659 658 680 684 681 53 1 657 659 658 680 681 684
54 1 681 683 682 699 703 700 54 1 681 683 682 699 700 703
55 1 700 702 701 718 722 719 55 1 700 702 701 718 719 722
56 1 719 721 720 738 742 739 56 1 719 721 720 738 739 742
57 2 724 727 725 726 733 728 57 2 724 727 725 726 728 733
58 2 724 726 725 727 734 729 58 2 724 726 725 727 729 734
59 2 725 733 726 728 735 730 59 2 725 733 726 728 730 735
60 2 725 734 727 729 736 730 60 2 725 734 727 729 730 736
61 2 726 735 728 730 737 729 61 2 726 735 728 730 729 737
62 2 727 736 729 730 737 728 62 2 727 736 729 730 728 737
63 1 739 741 740 748 752 749 63 1 739 741 740 748 749 752
64 1 749 751 750 755 759 756 64 1 749 751 750 755 756 759
65 1 756 758 757 777 781 778 65 1 756 758 757 777 778 781
66 1 778 780 779 794 798 795 66 1 778 780 779 794 795 798
67 1 784 786 785 787 793 792 67 1 784 786 785 787 792 793
68 1 795 797 796 813 817 814 68 1 795 797 796 813 814 817
69 1 814 816 815 828 832 829 69 1 814 816 815 828 829 832
70 1 829 831 830 840 844 841 70 1 829 831 830 840 841 844
71 1 841 843 842 847 851 848 71 1 841 843 842 847 848 851
72 1 848 850 849 871 875 872 72 1 848 850 849 871 872 875
73 1 872 874 873 885 889 886 73 1 872 874 873 885 886 889
74 1 886 888 887 904 908 905 74 1 886 888 887 904 905 908
75 1 905 907 906 915 919 916 75 1 905 907 906 915 916 919
76 1 916 918 917 927 931 928 76 1 916 918 917 927 928 931
77 1 928 930 929 948 952 949 77 1 928 930 929 948 949 952
78 2 933 936 934 935 943 937 78 2 933 936 934 935 937 943
79 2 933 935 934 936 944 938 79 2 933 935 934 936 938 944
80 2 934 943 935 937 945 939 80 2 934 943 935 937 939 945
81 2 934 944 936 938 946 939 81 2 934 944 936 938 939 946
82 2 935 945 937 939 940 938 82 2 935 945 937 939 938 940
83 2 936 946 938 939 940 937 83 2 936 946 938 939 937 940
84 1 949 951 950 962 966 963 84 1 949 951 950 962 963 966
85 1 954 956 955 957 961 960 85 1 954 956 955 957 960 961
86 1 963 965 964 981 985 982 86 1 963 965 964 981 982 985
87 1 982 984 983 998 1002 999 87 1 982 984 983 998 999 1002
88 1 988 990 989 991 997 996 88 1 988 990 989 991 996 997
89 1 999 1001 1000 1020 1024 1021 89 1 999 1001 1000 1020 1021 1024
90 1 1021 1023 1022 1035 1039 1036 90 1 1021 1023 1022 1035 1036 1039
91 1 1036 1038 1037 1046 1050 1047 91 1 1036 1038 1037 1046 1047 1050
92 1 1047 1049 1048 1060 1064 1061 92 1 1047 1049 1048 1060 1061 1064
93 1 1061 1063 1062 1079 1083 1080 93 1 1061 1063 1062 1079 1080 1083
94 1 1080 1082 1081 1097 1101 1098 94 1 1080 1082 1081 1097 1098 1101
95 4 1085 1088 1086 1087 1093 1089 95 4 1085 1088 1086 1087 1089 1093
96 5 1085 1087 1086 1088 1094 1090 96 5 1085 1087 1086 1088 1090 1094
97 6 1086 1093 1087 1089 1095 1090 97 6 1086 1093 1087 1089 1090 1095
98 4 1086 1094 1088 1090 1096 1089 98 4 1086 1094 1088 1090 1089 1096
99 6 1087 1095 1089 1090 1096 1088 99 6 1087 1095 1089 1090 1088 1096
100 1 1098 1100 1099 1116 1120 1117 100 1 1098 1100 1099 1116 1117 1120
101 1 1117 1119 1118 1132 1136 1133 101 1 1117 1119 1118 1132 1133 1136
102 1 1133 1135 1134 1151 1155 1152 102 1 1133 1135 1134 1151 1152 1155
103 1 1152 1154 1153 1175 1179 1176 103 1 1152 1154 1153 1175 1176 1179
104 1 1176 1178 1177 1194 1198 1195 104 1 1176 1178 1177 1194 1195 1198
105 1 1195 1197 1196 1218 1222 1219 105 1 1195 1197 1196 1218 1219 1222
106 1 1219 1221 1220 1225 1229 1226 106 1 1219 1221 1220 1225 1226 1229
PiTorsion Coeffs PiTorsion Coeffs

2
examples/amoeba/in.ubiquitin
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@ -29,7 +29,7 @@ read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit pitorsions PiTorsions & fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions fix bit bitorsions BiTorsions
pair_style amoeba include bitorsion pair_style amoeba include pitorsion
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes

2
src/AMOEBA/fix_amoeba_pitorsion.cpp
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@ -350,7 +350,7 @@ void FixAmoebaPiTorsion::post_force(int vflag)
ic = pitorsion_list[n][2]; ic = pitorsion_list[n][2];
id = pitorsion_list[n][3]; id = pitorsion_list[n][3];
ie = pitorsion_list[n][4]; ie = pitorsion_list[n][4];
ig = pitorsion_list[n][5]; ib = pitorsion_list[n][5];
ptype = pitorsion_list[n][6]; ptype = pitorsion_list[n][6];
// compute the value of the pi-system torsion angle // compute the value of the pi-system torsion angle

3
tools/tinker/tinker2lmp.py
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@ -755,8 +755,7 @@ for atom1 in id:
atom5 = bonds[atom2-1][0] atom5 = bonds[atom2-1][0]
atom6 = bonds[atom2-1][1] atom6 = bonds[atom2-1][1]
#pitorsionlist.append((atom3,atom4,atom1,atom2,atom5,atom6)) pitorsionlist.append((atom3,atom4,atom1,atom2,atom5,atom6))
pitorsionlist.append((atom3,atom4,atom1,atom2,atom6,atom5))
# create bitorslist = list of 5-body interactions # create bitorslist = list of 5-body interactions
# generate topology via double loop over neighbors of central atom3 # generate topology via double loop over neighbors of central atom3