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reading of bitorsion data file

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This commit is contained in:
Steve Plimpton
2022-03-14 18:08:14 -06:00
parent 1dda3055c2
commit 1d86b3e270
6 changed files with 2051 additions and 24 deletions
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1884
examples/amoeba/bitorsion.ubiquitin.data Normal file
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75
examples/amoeba/data.ubiquitin
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@ -14,6 +14,7 @@ LAMMPS data file created from Tinker ubiquitin.xyz and amoeba_ubiquitin.prm file
0 41.91 ylo yhi
0 41.91 zlo zhi
6 pitorsion types
106 bitorsions
106 pitorsions
Masses
@ -26348,6 +26349,80 @@ UreyBradley Coeffs
110 0.0 0.0
111 -7.6 1.5537
BiTorsions
1 1 3 20 21 22 37
2 1 22 37 38 39 56
3 1 39 56 57 58 76
4 1 58 76 77 78 92
5 1 78 92 93 94 114
6 1 94 114 115 116 128
7 1 116 128 129 130 147
8 1 130 147 148 149 161
9 2 149 161 162 163 168
10 1 163 168 169 170 190
11 1 170 190 191 192 204
12 1 192 204 205 206 223
13 1 206 223 224 225 237
14 1 225 237 238 239 256
15 1 239 256 257 258 271
16 1 258 271 272 273 287
17 3 273 287 288 289 302
18 1 304 316 317 318 327
19 1 318 327 328 329 339
20 1 329 339 340 341 353
21 1 341 353 354 355 372
22 1 355 372 373 374 387
23 1 374 387 388 389 401
24 1 389 401 402 403 417
25 1 403 417 418 419 439
26 1 419 439 440 441 449
27 1 441 449 450 451 471
28 1 451 471 472 473 490
29 1 473 490 491 492 507
30 1 492 507 508 509 519
31 1 509 519 520 521 541
32 1 521 541 542 543 556
33 2 543 556 557 558 563
34 3 558 563 564 565 582
35 1 598 610 611 612 622
36 1 612 622 623 624 639
37 1 624 639 640 641 656
38 1 641 656 657 658 680
39 1 658 680 681 682 699
40 1 682 699 700 701 718
41 1 701 718 719 720 738
42 1 720 738 739 740 748
43 2 740 748 749 750 755
44 1 750 755 756 757 777
45 1 757 777 778 779 794
46 1 779 794 795 796 813
47 1 796 813 814 815 828
48 1 815 828 829 830 840
49 2 830 840 841 842 847
50 1 842 847 848 849 871
51 1 849 871 872 873 885
52 1 873 885 886 887 904
53 1 887 904 905 906 915
54 1 906 915 916 917 927
55 1 917 927 928 929 948
56 1 929 948 949 950 962
57 1 950 962 963 964 981
58 1 964 981 982 983 998
59 1 983 998 999 1000 1020
60 1 1000 1020 1021 1022 1035
61 1 1022 1035 1036 1037 1046
62 1 1037 1046 1047 1048 1060
63 1 1048 1060 1061 1062 1079
64 1 1062 1079 1080 1081 1097
65 1 1081 1097 1098 1099 1116
66 1 1099 1116 1117 1118 1132
67 1 1118 1132 1133 1134 1151
68 1 1134 1151 1152 1153 1175
69 1 1153 1175 1176 1177 1194
70 1 1177 1194 1195 1196 1218
71 2 1196 1218 1219 1220 1225
PiTorsions
1 1 2 4 3 20 21 24

4
examples/amoeba/in.ubiquitin
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@ -16,6 +16,8 @@ improper_style amoeba
fix amtype all property/atom i_amtype ghost yes
fix pitorsion all pitorsion
fix_modify pitorsion energy yes
fix bitorsion all bitorsion bitorsion.ubiquitin.data
fix_modify bitorsion energy yes
fix extra all property/atom &
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
@ -26,7 +28,7 @@ read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pitorsion "pitorsion types" "PiTorsion Coeffs" &
fix pitorsion pitorsions PiTorsions
pair_style amoeba
pair_style amoeba include bitorsion
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes