From 501ef071c5279a0c9c57ab989c38f017ca56c5aa Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 21 Apr 2022 10:06:53 -0600 Subject: [PATCH] revert to original pitorsion code --- examples/amoeba/data.ubiquitin | 212 ++++++++++++++-------------- examples/amoeba/in.ubiquitin | 2 +- src/AMOEBA/fix_amoeba_pitorsion.cpp | 2 +- tools/tinker/tinker2lmp.py | 3 +- 4 files changed, 109 insertions(+), 110 deletions(-) diff --git a/examples/amoeba/data.ubiquitin b/examples/amoeba/data.ubiquitin index 653cbc3639..aada520e6d 100644 --- a/examples/amoeba/data.ubiquitin +++ b/examples/amoeba/data.ubiquitin @@ -26425,112 +26425,112 @@ BiTorsions PiTorsions -1 1 2 4 3 20 24 21 -2 1 21 23 22 37 41 38 -3 1 27 29 28 30 36 35 -4 1 38 40 39 56 60 57 -5 1 57 59 58 76 80 77 -6 2 62 65 63 64 71 66 -7 2 62 64 63 65 72 67 -8 2 63 71 64 66 73 68 -9 2 63 72 65 67 74 68 -10 2 64 73 66 68 75 67 -11 2 65 74 67 68 75 66 -12 1 77 79 78 92 96 93 -13 1 93 95 94 114 118 115 -14 1 115 117 116 128 132 129 -15 1 129 131 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+105 1 1195 1197 1196 1218 1219 1222 +106 1 1219 1221 1220 1225 1226 1229 PiTorsion Coeffs diff --git a/examples/amoeba/in.ubiquitin b/examples/amoeba/in.ubiquitin index e8516dc09c..cbae525bc1 100644 --- a/examples/amoeba/in.ubiquitin +++ b/examples/amoeba/in.ubiquitin @@ -29,7 +29,7 @@ read_data data.ubiquitin fix amtype NULL "Tinker Types" & fix pit pitorsions PiTorsions & fix bit bitorsions BiTorsions -pair_style amoeba include bitorsion +pair_style amoeba include pitorsion pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key special_bonds lj/coul 0.5 0.5 0.5 one/five yes diff --git a/src/AMOEBA/fix_amoeba_pitorsion.cpp b/src/AMOEBA/fix_amoeba_pitorsion.cpp index 19ec7e6786..014059661f 100644 --- a/src/AMOEBA/fix_amoeba_pitorsion.cpp +++ b/src/AMOEBA/fix_amoeba_pitorsion.cpp @@ -350,7 +350,7 @@ void FixAmoebaPiTorsion::post_force(int vflag) ic = pitorsion_list[n][2]; id = pitorsion_list[n][3]; ie = pitorsion_list[n][4]; - ig = pitorsion_list[n][5]; + ib = pitorsion_list[n][5]; ptype = pitorsion_list[n][6]; // compute the value of the pi-system torsion angle diff --git a/tools/tinker/tinker2lmp.py b/tools/tinker/tinker2lmp.py index 27376af0cf..3d871747b6 100644 --- a/tools/tinker/tinker2lmp.py +++ b/tools/tinker/tinker2lmp.py @@ -755,8 +755,7 @@ for atom1 in id: atom5 = bonds[atom2-1][0] atom6 = bonds[atom2-1][1] - #pitorsionlist.append((atom3,atom4,atom1,atom2,atom5,atom6)) - pitorsionlist.append((atom3,atom4,atom1,atom2,atom6,atom5)) + pitorsionlist.append((atom3,atom4,atom1,atom2,atom5,atom6)) # create bitorslist = list of 5-body interactions # generate topology via double loop over neighbors of central atom3