PLUMED-NEST by plumed-nest

Project ID: plumID:26.017
Source: interdomain_rotation/APO/2/plumed.dat
Originally used with PLUMED version: 2.9.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
#RESTART
# plumed.dat  –  replica 2
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps

The UNITS action with label  calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=../refs/monitor.dat
# The command:
# INCLUDE FILE=../refs/monitor.dat
# ensures PLUMED loads the contents of the file called ../refs/monitor.dat
# The contents of this file are shown below (click the red comment to hide them).
# monitor.dat  –  beta-arrestin 1 CVs
# INCLUDEd by every replica plumed.dat
#
# BIASED (see OPES blocks in plumed.dat):
#   all replicas : p_rmsd_twist_l0p1.s  dist_R62_D67  dist_R76_D69
#   replicas 1-4 : R169_D290  R169_D26  theta_rev
#   replicas 3-4 : cmap_holo_specific  cmap_apo_specific

The INCLUDE action with label ../refs/monitor.dat calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps

#  loop COMs (monitor) 
gFL: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1089,1108,1120,1136,1155,1162,1181,1195  # finger loop CA 68-75
The GROUP action with label gFL calculates somethinggML: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2171,2183,2197,2204,2226,2236,2247,2254,2270,2282,2303  # middle loop CA 135-145
The GROUP action with label gML calculates somethinggLR: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=4654,4666,4673,4695,4714,4736,4753,4768  # lariat loop CA 290-297
The GROUP action with label gLR calculates somethingCOM_FL: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gFL NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label COM_FL calculates somethingCOM_ML: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gML NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label COM_ML calculates somethingCOM_LR: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gLR NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label COM_LR calculates somethingd_FL_LR: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_FL,COM_LR NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d_FL_LR calculates the following quantities: Quantity    Description  
d_FL_LR.value the DISTANCE between this pair of atomsd_FL_ML: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_FL,COM_ML NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d_FL_ML calculates the following quantities: Quantity    Description  
d_FL_ML.value the DISTANCE between this pair of atomsd_ML_LR: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_ML,COM_LR NOPBC ignore the periodic boundary conditions when calculating distances

#  sidechain COM groups 
The DISTANCE action with label d_ML_LR calculates the following quantities: Quantity    Description  
d_ML_LR.value the DISTANCE between this pair of atomsSC_THR6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=72,74,76 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_THR6 calculates somethingSC_ARG7: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=86,89,92,95,97-98,101 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG7 calculates somethingSC_VAL8: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=110,112,116 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_VAL8 calculates somethingSC_LYS10: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=146,149,152,155,158 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LYS10 calculates somethingSC_TYR21: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=317,320-321,323,325-326,328,330 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_TYR21 calculates somethingSC_ARG25: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=386,389,392,395,397-398,401 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG25 calculates somethingSC_ASP26: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=410,413-415 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP26 calculates somethingSC_ASP29: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=458,461-463 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP29 calculates somethingSC_LEU42: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=646,649,651,655 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LEU42 calculates somethingSC_TYR47: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=722,725-726,728,730-731,733,735 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_TYR47 calculates somethingSC_ARG52: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=823,826,829,832,834-835,838 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG52 calculates somethingSC_VAL55: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=884,886,890 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_VAL55 calculates somethingSC_ARG62: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=988,991,994,997,999-1000,1003 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG62 calculates somethingSC_TYR63: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1012,1015-1016,1018,1020-1021,1023,1025 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_TYR63 calculates somethingSC_GLY64: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1031 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLY64 calculates somethingSC_GLU66: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1064,1067,1070-1072 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLU66 calculates somethingSC_ASP67: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1079,1082-1084 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP67 calculates somethingSC_ASP69: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1110,1113-1115 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP69 calculates somethingSC_GLY72: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1155 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLY72 calculates somethingSC_THR74: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1183,1185,1187 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_THR74 calculates somethingSC_ARG76: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1217,1220,1223,1226,1228-1229,1232 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG76 calculates somethingSC_LYS77: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1241,1244,1247,1250,1253 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LYS77 calculates somethingSC_GLN85: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1370,1373,1376-1378 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLN85 calculates somethingSC_LEU100: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1612,1615,1617,1621 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LEU100 calculates somethingSC_LYS106: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1725,1728,1731,1734,1737 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LYS106 calculates somethingSC_SER126: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2046,2049 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_SER126 calculates somethingSC_THR128: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2073,2075,2077 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_THR128 calculates somethingSC_GLN130: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2106,2109,2112-2114 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLN130 calculates somethingSC_PRO131: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2120,2125,2128 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_PRO131 calculates somethingSC_THR136: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2185,2187,2189 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_THR136 calculates somethingSC_LYS138: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2206,2209,2212,2215,2218 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LYS138 calculates somethingSC_ALA139: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2228 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ALA139 calculates somethingSC_CYS140: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2238,2241 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_CYS140 calculates somethingSC_VAL167: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2683,2685,2689 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_VAL167 calculates somethingSC_ARG169: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2718,2721,2724,2727,2729-2730,2733 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG169 calculates somethingSC_LYS170: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2742,2745,2748,2751,2754 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LYS170 calculates somethingSC_PRO178: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2878,2883,2886 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_PRO178 calculates somethingSC_GLN181: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2916,2919,2922-2924 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLN181 calculates somethingSC_PRO182: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2930,2935,2938 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_PRO182 calculates somethingSC_THR183: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2947,2949,2951 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_THR183 calculates somethingSC_ALA184: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2961 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ALA184 calculates somethingSC_GLU185: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2971,2974,2977-2979 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLU185 calculates somethingSC_THR186: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2986,2988,2990 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_THR186 calculates somethingSC_THR187: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3000,3002,3004 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_THR187 calculates somethingSC_ARG188: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3014,3017,3020,3023,3025-3026,3029 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG188 calculates somethingSC_GLN189: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3038,3041,3044-3046 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLN189 calculates somethingSC_ASP194: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3122,3125-3127 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP194 calculates somethingSC_LEU197: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3170,3173,3175,3179 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LEU197 calculates somethingSC_HIS198: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3189,3192,3194-3195,3197-3198 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_HIS198 calculates somethingSC_LEU199: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3206,3209,3211,3215 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LEU199 calculates somethingSC_ALA201: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3240 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ALA201 calculates somethingSC_LEU203: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3261,3264,3266,3270 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LEU203 calculates somethingSC_ILE207: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3329,3331,3335,3338 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ILE207 calculates somethingSC_ASN225: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3608,3611-3613 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASN225 calculates somethingSC_ILE241: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3889,3891,3895,3898 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ILE241 calculates somethingSC_GLN248: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4001,4004,4007-4009 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLN248 calculates somethingSC_ARG282: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4516,4519,4522,4525,4527-4528,4531 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG282 calculates somethingSC_LYS284: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4555,4558,4561,4564,4567 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LYS284 calculates somethingSC_ASP290: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4656,4659-4661 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP290 calculates somethingSC_GLY291: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4666 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLY291 calculates somethingSC_LYS292: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4675,4678,4681,4684,4687 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LYS292 calculates somethingSC_LEU293: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4697,4700,4702,4706 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LEU293 calculates somethingSC_LYS294: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4716,4719,4722,4725,4728 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LYS294 calculates somethingSC_HIS295: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4738,4741,4743-4744,4746-4747 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_HIS295 calculates somethingSC_GLU296: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4755,4758,4761-4763 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLU296 calculates somethingSC_ASP297: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4770,4773-4775 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP297 calculates somethingSC_THR298: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=4782,4784,4786 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_THR298 calculates somethingSC_GLU313: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5007,5010,5013-5015 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLU313 calculates somethingSC_LEU315: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5041,5044,5046,5050 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_LEU315 calculates somethingSC_ILE317: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5067,5069,5073,5076 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ILE317 calculates somethingSC_ASP385: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6128,6131-6133 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP385 calculates somethingSC_VAL387: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6159,6161,6165 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_VAL387 calculates somethingSC_PHE388: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6175,6178-6179,6181,6183,6185,6187 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_PHE388 calculates somethingSC_GLU389: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6195,6198,6201-6203 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLU389 calculates somethingSC_ASP390: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6210,6213-6215 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ASP390 calculates somethingSC_PHE391: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6222,6225-6226,6228,6230,6232,6234 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_PHE391 calculates somethingSC_ARG393: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6252,6255,6258,6261,6263-6264,6267 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_ARG393 calculates somethingSC_GLN394: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6276,6279,6282-6284 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label SC_GLN394 calculates somethingSC_LEU396: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=6317,6320,6322,6326,6332,6334 NOPBC ignore the periodic boundary conditions when calculating distances

#  sidechain-COM distances 
The COM action with label SC_LEU396 calculates somethingK77_E313: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LYS77,SC_GLU313 NOPBC ignore the periodic boundary conditions when calculating distances  # polar core
The DISTANCE action with label K77_E313 calculates the following quantities: Quantity    Description  
K77_E313.value the DISTANCE between this pair of atomsR169_D290: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG169,SC_ASP290 NOPBC ignore the periodic boundary conditions when calculating distances  # polar core  ← BIASED r1-4
The DISTANCE action with label R169_D290 calculates the following quantities: Quantity    Description  
R169_D290.value the DISTANCE between this pair of atomsR169_D26: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG169,SC_ASP26 NOPBC ignore the periodic boundary conditions when calculating distances  # polar core  ← BIASED r1-4
The DISTANCE action with label R169_D26 calculates the following quantities: Quantity    Description  
R169_D26.value the DISTANCE between this pair of atomsR25_D297: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG25,SC_ASP297 NOPBC ignore the periodic boundary conditions when calculating distances  # polar core
The DISTANCE action with label R25_D297 calculates the following quantities: Quantity    Description  
R25_D297.value the DISTANCE between this pair of atomsD29_K170: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ASP29,SC_LYS170 NOPBC ignore the periodic boundary conditions when calculating distances  # polar core
The DISTANCE action with label D29_K170 calculates the following quantities: Quantity    Description  
D29_K170.value the DISTANCE between this pair of atomsdist_R62_D67: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG62,SC_ASP67 NOPBC ignore the periodic boundary conditions when calculating distances  # ionic lock  ← BIASED all
The DISTANCE action with label dist_R62_D67 calculates the following quantities: Quantity    Description  
dist_R62_D67.value the DISTANCE between this pair of atomsdist_R76_D69: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG76,SC_ASP69 NOPBC ignore the periodic boundary conditions when calculating distances  # ionic lock  ← BIASED all
The DISTANCE action with label dist_R76_D69 calculates the following quantities: Quantity    Description  
dist_R76_D69.value the DISTANCE between this pair of atomsK10_D390: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LYS10,SC_ASP390 NOPBC ignore the periodic boundary conditions when calculating distances  # C-tail
The DISTANCE action with label K10_D390 calculates the following quantities: Quantity    Description  
K10_D390.value the DISTANCE between this pair of atomsK10_E389: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LYS10,SC_GLU389 NOPBC ignore the periodic boundary conditions when calculating distances  # C-tail apo salt
The DISTANCE action with label K10_E389 calculates the following quantities: Quantity    Description  
K10_E389.value the DISTANCE between this pair of atomsR393_D26: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG393,SC_ASP26 NOPBC ignore the periodic boundary conditions when calculating distances  # gate-loop → polar core
The DISTANCE action with label R393_D26 calculates the following quantities: Quantity    Description  
R393_D26.value the DISTANCE between this pair of atomsR393_D297: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG393,SC_ASP297 NOPBC ignore the periodic boundary conditions when calculating distances  # C-tail apo
The DISTANCE action with label R393_D297 calculates the following quantities: Quantity    Description  
R393_D297.value the DISTANCE between this pair of atomsR25_V167: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG25,SC_VAL167 NOPBC ignore the periodic boundary conditions when calculating distances  # holo HB Δ+97%
The DISTANCE action with label R25_V167 calculates the following quantities: Quantity    Description  
R25_V167.value the DISTANCE between this pair of atomsR169_G291: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG169,SC_GLY291 NOPBC ignore the periodic boundary conditions when calculating distances  # holo HB Δ+61%
The DISTANCE action with label R169_G291 calculates the following quantities: Quantity    Description  
R169_G291.value the DISTANCE between this pair of atomsQ189_L197: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_GLN189,SC_LEU197 NOPBC ignore the periodic boundary conditions when calculating distances  # apo HB Δ-100%
The DISTANCE action with label Q189_L197 calculates the following quantities: Quantity    Description  
Q189_L197.value the DISTANCE between this pair of atomsR169_D297: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG169,SC_ASP297 NOPBC ignore the periodic boundary conditions when calculating distances  # apo HB Δ-80%
The DISTANCE action with label R169_D297 calculates the following quantities: Quantity    Description  
R169_D297.value the DISTANCE between this pair of atomsQ394_E296: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_GLN394,SC_GLU296 NOPBC ignore the periodic boundary conditions when calculating distances  # apo HB Δ-70%
The DISTANCE action with label Q394_E296 calculates the following quantities: Quantity    Description  
Q394_E296.value the DISTANCE between this pair of atomsH295_T298: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_HIS295,SC_THR298 NOPBC ignore the periodic boundary conditions when calculating distances  # apo HB Δ-60%
The DISTANCE action with label H295_T298 calculates the following quantities: Quantity    Description  
H295_T298.value the DISTANCE between this pair of atomsN225_D194: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ASN225,SC_ASP194 NOPBC ignore the periodic boundary conditions when calculating distances  # apo HB Δ-52%
The DISTANCE action with label N225_D194 calculates the following quantities: Quantity    Description  
N225_D194.value the DISTANCE between this pair of atomsK10_F391: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LYS10,SC_PHE391 NOPBC ignore the periodic boundary conditions when calculating distances  # apo Δ-88%
The DISTANCE action with label K10_F391 calculates the following quantities: Quantity    Description  
K10_F391.value the DISTANCE between this pair of atomsD385_T6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ASP385,SC_THR6 NOPBC ignore the periodic boundary conditions when calculating distances  # apo HB Δ-63%
The DISTANCE action with label D385_T6 calculates the following quantities: Quantity    Description  
D385_T6.value the DISTANCE between this pair of atomsR7_V387: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG7,SC_VAL387 NOPBC ignore the periodic boundary conditions when calculating distances  # N-domain contact (resid387=VAL in PDB)
The DISTANCE action with label R7_V387 calculates the following quantities: Quantity    Description  
R7_V387.value the DISTANCE between this pair of atomsL396_K294: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LEU396,SC_LYS294 NOPBC ignore the periodic boundary conditions when calculating distances  # C-tail cap (resid396=LEU, 294=LYS in PDB)
The DISTANCE action with label L396_K294 calculates the following quantities: Quantity    Description  
L396_K294.value the DISTANCE between this pair of atomsI317_L315: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ILE317,SC_LEU315 NOPBC ignore the periodic boundary conditions when calculating distances  # apo Δ-48%  hydrophobic core
The DISTANCE action with label I317_L315 calculates the following quantities: Quantity    Description  
I317_L315.value the DISTANCE between this pair of atomsK10_D390_2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LYS10,SC_ASP390 NOPBC ignore the periodic boundary conditions when calculating distances  # C-tail (dup ok)
The DISTANCE action with label K10_D390_2 calculates the following quantities: Quantity    Description  
K10_D390_2.value the DISTANCE between this pair of atomsR393_D297_2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG393,SC_ASP297 NOPBC ignore the periodic boundary conditions when calculating distances  # C-tail (dup ok)
The DISTANCE action with label R393_D297_2 calculates the following quantities: Quantity    Description  
R393_D297_2.value the DISTANCE between this pair of atomsR62_D67_lock: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG62,SC_ASP67 NOPBC ignore the periodic boundary conditions when calculating distances  # ionic lock (dup ok)
The DISTANCE action with label R62_D67_lock calculates the following quantities: Quantity    Description  
R62_D67_lock.value the DISTANCE between this pair of atomsR76_D69_lock: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_ARG76,SC_ASP69 NOPBC ignore the periodic boundary conditions when calculating distances  # ionic lock (dup ok)
The DISTANCE action with label R76_D69_lock calculates the following quantities: Quantity    Description  
R76_D69_lock.value the DISTANCE between this pair of atomsY63_K138: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_TYR63,SC_LYS138 NOPBC ignore the periodic boundary conditions when calculating distances  # contact
The DISTANCE action with label Y63_K138 calculates the following quantities: Quantity    Description  
Y63_K138.value the DISTANCE between this pair of atomsP131_K138: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_PRO131,SC_LYS138 NOPBC ignore the periodic boundary conditions when calculating distances  # contact
The DISTANCE action with label P131_K138 calculates the following quantities: Quantity    Description  
P131_K138.value the DISTANCE between this pair of atomsL42_Y21: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LEU42,SC_TYR21 NOPBC ignore the periodic boundary conditions when calculating distances  # packing
The DISTANCE action with label L42_Y21 calculates the following quantities: Quantity    Description  
L42_Y21.value the DISTANCE between this pair of atomsY21_F388: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_TYR21,SC_PHE388 NOPBC ignore the periodic boundary conditions when calculating distances  # packing
The DISTANCE action with label Y21_F388 calculates the following quantities: Quantity    Description  
Y21_F388.value the DISTANCE between this pair of atomsF388_V8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_PHE388,SC_VAL8 NOPBC ignore the periodic boundary conditions when calculating distances  # packing
The DISTANCE action with label F388_V8 calculates the following quantities: Quantity    Description  
F388_V8.value the DISTANCE between this pair of atomsV8_E389: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_VAL8,SC_GLU389 NOPBC ignore the periodic boundary conditions when calculating distances  # contact
The DISTANCE action with label V8_E389 calculates the following quantities: Quantity    Description  
V8_E389.value the DISTANCE between this pair of atomsL106_Y21: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LYS106,SC_TYR21 NOPBC ignore the periodic boundary conditions when calculating distances  # packing
The DISTANCE action with label L106_Y21 calculates the following quantities: Quantity    Description  
L106_Y21.value the DISTANCE between this pair of atomsL100_V8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=SC_LEU100,SC_VAL8 NOPBC ignore the periodic boundary conditions when calculating distances  # packing

#  atom–atom distances 
The DISTANCE action with label L100_V8 calculates the following quantities: Quantity    Description  
L100_V8.value the DISTANCE between this pair of atomsK77_E313_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1253,5014 NOPBC ignore the periodic boundary conditions when calculating distances  # res77:NZ – res313:OE1
The DISTANCE action with label K77_E313_at calculates the following quantities: Quantity    Description  
K77_E313_at.value the DISTANCE between this pair of atomsR169_D290_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2730,4660 NOPBC ignore the periodic boundary conditions when calculating distances  # res169:NH1 – res290:OD1
The DISTANCE action with label R169_D290_at calculates the following quantities: Quantity    Description  
R169_D290_at.value the DISTANCE between this pair of atomsR169_D26_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2730,414 NOPBC ignore the periodic boundary conditions when calculating distances  # res169:NH1 – res26:OD1
The DISTANCE action with label R169_D26_at calculates the following quantities: Quantity    Description  
R169_D26_at.value the DISTANCE between this pair of atomsR25_D297_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=398,4774 NOPBC ignore the periodic boundary conditions when calculating distances  # res25:NH1 – res297:OD1
The DISTANCE action with label R25_D297_at calculates the following quantities: Quantity    Description  
R25_D297_at.value the DISTANCE between this pair of atomsD29_K170_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=462,2754 NOPBC ignore the periodic boundary conditions when calculating distances  # res29:OD1 – res170:NZ
The DISTANCE action with label D29_K170_at calculates the following quantities: Quantity    Description  
D29_K170_at.value the DISTANCE between this pair of atomsD26_D290_CG: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=413,4659 NOPBC ignore the periodic boundary conditions when calculating distances  # res26:CG – res290:CG
The DISTANCE action with label D26_D290_CG calculates the following quantities: Quantity    Description  
D26_D290_CG.value the DISTANCE between this pair of atomsD26_D297_CG: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=413,4773 NOPBC ignore the periodic boundary conditions when calculating distances  # res26:CG – res297:CG
The DISTANCE action with label D26_D297_CG calculates the following quantities: Quantity    Description  
D26_D297_CG.value the DISTANCE between this pair of atomsR62_D67_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1000,1083 NOPBC ignore the periodic boundary conditions when calculating distances  # res62:NH1 – res67:OD1
The DISTANCE action with label R62_D67_at calculates the following quantities: Quantity    Description  
R62_D67_at.value the DISTANCE between this pair of atomsR76_D69_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1229,1114 NOPBC ignore the periodic boundary conditions when calculating distances  # res76:NH1 – res69:OD1
The DISTANCE action with label R76_D69_at calculates the following quantities: Quantity    Description  
R76_D69_at.value the DISTANCE between this pair of atomsK10_D390_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=158,6214 NOPBC ignore the periodic boundary conditions when calculating distances  # res10:NZ – res390:OD1
The DISTANCE action with label K10_D390_at calculates the following quantities: Quantity    Description  
K10_D390_at.value the DISTANCE between this pair of atomsK10_E389_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=158,6202 NOPBC ignore the periodic boundary conditions when calculating distances  # res10:NZ – res389:OE1
The DISTANCE action with label K10_E389_at calculates the following quantities: Quantity    Description  
K10_E389_at.value the DISTANCE between this pair of atomsR393_D26_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6264,414 NOPBC ignore the periodic boundary conditions when calculating distances  # res393:NH1 – res26:OD1
The DISTANCE action with label R393_D26_at calculates the following quantities: Quantity    Description  
R393_D26_at.value the DISTANCE between this pair of atomsR393_D297_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6264,4774 NOPBC ignore the periodic boundary conditions when calculating distances  # res393:NH1 – res297:OD1
The DISTANCE action with label R393_D297_at calculates the following quantities: Quantity    Description  
R393_D297_at.value the DISTANCE between this pair of atomsR25_V167_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=398,2685 NOPBC ignore the periodic boundary conditions when calculating distances  # res25:NH1 – res167:CG1
The DISTANCE action with label R25_V167_at calculates the following quantities: Quantity    Description  
R25_V167_at.value the DISTANCE between this pair of atomsQ189_L197_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3046,3175 NOPBC ignore the periodic boundary conditions when calculating distances  # res189:NE2 – res197:CD1
The DISTANCE action with label Q189_L197_at calculates the following quantities: Quantity    Description  
Q189_L197_at.value the DISTANCE between this pair of atomsR169_D297_at2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2730,4774 NOPBC ignore the periodic boundary conditions when calculating distances  # res169:NH1 – res297:OD1
The DISTANCE action with label R169_D297_at2 calculates the following quantities: Quantity    Description  
R169_D297_at2.value the DISTANCE between this pair of atomsQ394_E296_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6284,4762 NOPBC ignore the periodic boundary conditions when calculating distances  # res394:NE2 – res296:OE1
The DISTANCE action with label Q394_E296_at calculates the following quantities: Quantity    Description  
Q394_E296_at.value the DISTANCE between this pair of atomsH295_T298_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4741,4784 NOPBC ignore the periodic boundary conditions when calculating distances  # res295:ND1 – res298:OG1
The DISTANCE action with label H295_T298_at calculates the following quantities: Quantity    Description  
H295_T298_at.value the DISTANCE between this pair of atomsN225_D194_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3613,3126 NOPBC ignore the periodic boundary conditions when calculating distances  # res225:ND2 – res194:OD1
The DISTANCE action with label N225_D194_at calculates the following quantities: Quantity    Description  
N225_D194_at.value the DISTANCE between this pair of atomsR7_V387_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=98,6161 NOPBC ignore the periodic boundary conditions when calculating distances  # res7:NH1 – res387:CG1
The DISTANCE action with label R7_V387_at calculates the following quantities: Quantity    Description  
R7_V387_at.value the DISTANCE between this pair of atomsL396_K294_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6322,4728 NOPBC ignore the periodic boundary conditions when calculating distances  # res396:CD1 – res294:NZ
The DISTANCE action with label L396_K294_at calculates the following quantities: Quantity    Description  
L396_K294_at.value the DISTANCE between this pair of atomsR169_G291_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2730,4666 NOPBC ignore the periodic boundary conditions when calculating distances  # res169:NH1 – res291:CA
The DISTANCE action with label R169_G291_at calculates the following quantities: Quantity    Description  
R169_G291_at.value the DISTANCE between this pair of atomsK10_F391_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=158,6230 NOPBC ignore the periodic boundary conditions when calculating distances  # res10:NZ – res391:CZ
The DISTANCE action with label K10_F391_at calculates the following quantities: Quantity    Description  
K10_F391_at.value the DISTANCE between this pair of atomsD385_T6_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6132,74 NOPBC ignore the periodic boundary conditions when calculating distances  # res385:OD1 – res6:OG1
The DISTANCE action with label D385_T6_at calculates the following quantities: Quantity    Description  
D385_T6_at.value the DISTANCE between this pair of atomsI317_L315_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5076,5046 NOPBC ignore the periodic boundary conditions when calculating distances  # res317:CD – res315:CD1
The DISTANCE action with label I317_L315_at calculates the following quantities: Quantity    Description  
I317_L315_at.value the DISTANCE between this pair of atomsY63_K138_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1021,2218 NOPBC ignore the periodic boundary conditions when calculating distances  # res63:OH – res138:NZ
The DISTANCE action with label Y63_K138_at calculates the following quantities: Quantity    Description  
Y63_K138_at.value the DISTANCE between this pair of atomsP131_K138_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2123,2218 NOPBC ignore the periodic boundary conditions when calculating distances  # res131:CA – res138:NZ
The DISTANCE action with label P131_K138_at calculates the following quantities: Quantity    Description  
P131_K138_at.value the DISTANCE between this pair of atomsL42_Y21_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=644,315 NOPBC ignore the periodic boundary conditions when calculating distances  # res42:CA – res21:CA
The DISTANCE action with label L42_Y21_at calculates the following quantities: Quantity    Description  
L42_Y21_at.value the DISTANCE between this pair of atomsY21_F388_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=315,6173 NOPBC ignore the periodic boundary conditions when calculating distances  # res21:CA – res388:CA
The DISTANCE action with label Y21_F388_at calculates the following quantities: Quantity    Description  
Y21_F388_at.value the DISTANCE between this pair of atomsF388_V8_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6173,108 NOPBC ignore the periodic boundary conditions when calculating distances  # res388:CA – res8:CA
The DISTANCE action with label F388_V8_at calculates the following quantities: Quantity    Description  
F388_V8_at.value the DISTANCE between this pair of atomsV8_E389_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=108,6193 NOPBC ignore the periodic boundary conditions when calculating distances  # res8:CA – res389:CA
The DISTANCE action with label V8_E389_at calculates the following quantities: Quantity    Description  
V8_E389_at.value the DISTANCE between this pair of atomsL106_Y21_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1723,315 NOPBC ignore the periodic boundary conditions when calculating distances  # res106:CA – res21:CA
The DISTANCE action with label L106_Y21_at calculates the following quantities: Quantity    Description  
L106_Y21_at.value the DISTANCE between this pair of atomsL100_V8_at: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1610,108 NOPBC ignore the periodic boundary conditions when calculating distances  # res100:CA – res8:CA

#  state CMAPs  (biased replicas 3-4) 
# RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12

The DISTANCE action with label L100_V8_at calculates the following quantities: Quantity    Description  
L100_V8_at.value the DISTANCE between this pair of atomscmap_holo_specific: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
  ATOMS1the atoms involved in each of the contacts you wish to calculate=SC_ALA184,SC_ALA201 REFERENCE1A reference value for a given contact, by default is 0=0.950000 WEIGHT1A weight value for a given contact, by default is 1=1.0 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 184-201
  ATOMS2the atoms involved in each of the contacts you wish to calculate=SC_ARG188,SC_LEU197 REFERENCE2A reference value for a given contact, by default is 0=0.950000 WEIGHT2A weight value for a given contact, by default is 1=1.0 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 188-197
  ATOMS3the atoms involved in each of the contacts you wish to calculate=SC_ARG25,SC_VAL167 REFERENCE3A reference value for a given contact, by default is 0=0.950000 WEIGHT3A weight value for a given contact, by default is 1=1.0 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 25-167
  ATOMS4the atoms involved in each of the contacts you wish to calculate=SC_PRO182,SC_LEU203 REFERENCE4A reference value for a given contact, by default is 0=0.950000 WEIGHT4A weight value for a given contact, by default is 1=1.0 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 182-203
  ATOMS5the atoms involved in each of the contacts you wish to calculate=SC_ARG169,SC_GLY291 REFERENCE5A reference value for a given contact, by default is 0=0.950000 WEIGHT5A weight value for a given contact, by default is 1=1.0 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 169-291
  ATOMS6the atoms involved in each of the contacts you wish to calculate=SC_GLN181,SC_LEU203 REFERENCE6A reference value for a given contact, by default is 0=0.950000 WEIGHT6A weight value for a given contact, by default is 1=1.0 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 181-203
  ATOMS7the atoms involved in each of the contacts you wish to calculate=SC_ARG62,SC_THR74 REFERENCE7A reference value for a given contact, by default is 0=0.950000 WEIGHT7A weight value for a given contact, by default is 1=1.0 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 62-74
  ATOMS8the atoms involved in each of the contacts you wish to calculate=SC_SER126,SC_GLY291 REFERENCE8A reference value for a given contact, by default is 0=0.950000 WEIGHT8A weight value for a given contact, by default is 1=1.0 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 126-291
  ATOMS9the atoms involved in each of the contacts you wish to calculate=SC_THR128,SC_CYS140 REFERENCE9A reference value for a given contact, by default is 0=0.950000 WEIGHT9A weight value for a given contact, by default is 1=1.0 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 128-140
  ATOMS10the atoms involved in each of the contacts you wish to calculate=SC_GLN130,SC_LYS284 REFERENCE10A reference value for a given contact, by default is 0=0.950000 WEIGHT10A weight value for a given contact, by default is 1=1.0 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 130-284
  ATOMS11the atoms involved in each of the contacts you wish to calculate=SC_ILE241,SC_GLN248 REFERENCE11A reference value for a given contact, by default is 0=0.950000 WEIGHT11A weight value for a given contact, by default is 1=1.0 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 241-248
  ATOMS12the atoms involved in each of the contacts you wish to calculate=SC_PRO178,SC_ILE207 REFERENCE12A reference value for a given contact, by default is 0=0.950000 WEIGHT12A weight value for a given contact, by default is 1=1.0 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 178-207
  ATOMS13the atoms involved in each of the contacts you wish to calculate=SC_LEU293,SC_GLU296 REFERENCE13A reference value for a given contact, by default is 0=0.950000 WEIGHT13A weight value for a given contact, by default is 1=1.0 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 293-296
  ATOMS14the atoms involved in each of the contacts you wish to calculate=SC_VAL55,SC_GLN85 REFERENCE14A reference value for a given contact, by default is 0=0.950000 WEIGHT14A weight value for a given contact, by default is 1=1.0 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 55-85
  ATOMS15the atoms involved in each of the contacts you wish to calculate=SC_GLN130,SC_PRO131 REFERENCE15A reference value for a given contact, by default is 0=0.950000 WEIGHT15A weight value for a given contact, by default is 1=1.0 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 130-131
  ATOMS16the atoms involved in each of the contacts you wish to calculate=SC_THR186,SC_HIS198 REFERENCE16A reference value for a given contact, by default is 0=0.950000 WEIGHT16A weight value for a given contact, by default is 1=1.0 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 186-198
  ATOMS17the atoms involved in each of the contacts you wish to calculate=SC_GLY72,SC_THR136 REFERENCE17A reference value for a given contact, by default is 0=0.950000 WEIGHT17A weight value for a given contact, by default is 1=1.0 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 72-136
  ATOMS18the atoms involved in each of the contacts you wish to calculate=SC_ARG282,SC_ASP297 REFERENCE18A reference value for a given contact, by default is 0=0.950000 WEIGHT18A weight value for a given contact, by default is 1=1.0 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 282-297
  ATOMS19the atoms involved in each of the contacts you wish to calculate=SC_TYR47,SC_ARG52 REFERENCE19A reference value for a given contact, by default is 0=0.950000 WEIGHT19A weight value for a given contact, by default is 1=1.0 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 47-52
  ATOMS20the atoms involved in each of the contacts you wish to calculate=SC_ASP290,SC_THR298 REFERENCE20A reference value for a given contact, by default is 0=0.950000 WEIGHT20A weight value for a given contact, by default is 1=1.0 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 290-298
  CMDIST calculate the distance with respect to the provided reference contact map
...

The CONTACTMAP action with label cmap_holo_specific calculates the following quantities: Quantity    Description  
cmap_holo_specific.contact By not using SUM or CMDIST each contact will be stored in a component
cmap_holo_specific.value the sum of all the switching function on all the distancescmap_apo_specific: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
  ATOMS1the atoms involved in each of the contacts you wish to calculate=SC_GLN189,SC_LEU197 REFERENCE1A reference value for a given contact, by default is 0=0.950000 WEIGHT1A weight value for a given contact, by default is 1=1.0 SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 189-197
  ATOMS2the atoms involved in each of the contacts you wish to calculate=SC_THR187,SC_LEU199 REFERENCE2A reference value for a given contact, by default is 0=0.950000 WEIGHT2A weight value for a given contact, by default is 1=1.0 SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 187-199
  ATOMS3the atoms involved in each of the contacts you wish to calculate=SC_GLU185,SC_ALA201 REFERENCE3A reference value for a given contact, by default is 0=0.950000 WEIGHT3A weight value for a given contact, by default is 1=1.0 SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 185-201
  ATOMS4the atoms involved in each of the contacts you wish to calculate=SC_VAL8,SC_GLU389 REFERENCE4A reference value for a given contact, by default is 0=0.950000 WEIGHT4A weight value for a given contact, by default is 1=1.0 SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 8-389
  ATOMS5the atoms involved in each of the contacts you wish to calculate=SC_VAL8,SC_VAL387 REFERENCE5A reference value for a given contact, by default is 0=0.950000 WEIGHT5A weight value for a given contact, by default is 1=1.0 SWITCH5The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 8-387
  ATOMS6the atoms involved in each of the contacts you wish to calculate=SC_THR6,SC_VAL387 REFERENCE6A reference value for a given contact, by default is 0=0.950000 WEIGHT6A weight value for a given contact, by default is 1=1.0 SWITCH6The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 6-387
  ATOMS7the atoms involved in each of the contacts you wish to calculate=SC_LYS10,SC_GLU389 REFERENCE7A reference value for a given contact, by default is 0=0.950000 WEIGHT7A weight value for a given contact, by default is 1=1.0 SWITCH7The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 10-389
  ATOMS8the atoms involved in each of the contacts you wish to calculate=SC_GLY64,SC_ALA139 REFERENCE8A reference value for a given contact, by default is 0=0.950000 WEIGHT8A weight value for a given contact, by default is 1=1.0 SWITCH8The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 64-139
  ATOMS9the atoms involved in each of the contacts you wish to calculate=SC_LYS10,SC_PHE391 REFERENCE9A reference value for a given contact, by default is 0=0.950000 WEIGHT9A weight value for a given contact, by default is 1=1.0 SWITCH9The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 10-391
  ATOMS10the atoms involved in each of the contacts you wish to calculate=SC_ARG169,SC_ASP297 REFERENCE10A reference value for a given contact, by default is 0=0.950000 WEIGHT10A weight value for a given contact, by default is 1=1.0 SWITCH10The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 169-297
  ATOMS11the atoms involved in each of the contacts you wish to calculate=SC_ARG25,SC_PHE391 REFERENCE11A reference value for a given contact, by default is 0=0.950000 WEIGHT11A weight value for a given contact, by default is 1=1.0 SWITCH11The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 25-391
  ATOMS12the atoms involved in each of the contacts you wish to calculate=SC_ASP26,SC_ARG393 REFERENCE12A reference value for a given contact, by default is 0=0.950000 WEIGHT12A weight value for a given contact, by default is 1=1.0 SWITCH12The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 26-393
  ATOMS13the atoms involved in each of the contacts you wish to calculate=SC_ARG25,SC_ASP297 REFERENCE13A reference value for a given contact, by default is 0=0.950000 WEIGHT13A weight value for a given contact, by default is 1=1.0 SWITCH13The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 25-297
  ATOMS14the atoms involved in each of the contacts you wish to calculate=SC_LYS294,SC_LEU396 REFERENCE14A reference value for a given contact, by default is 0=0.950000 WEIGHT14A weight value for a given contact, by default is 1=1.0 SWITCH14The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 294-396
  ATOMS15the atoms involved in each of the contacts you wish to calculate=SC_GLU296,SC_GLN394 REFERENCE15A reference value for a given contact, by default is 0=0.950000 WEIGHT15A weight value for a given contact, by default is 1=1.0 SWITCH15The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 296-394
  ATOMS16the atoms involved in each of the contacts you wish to calculate=SC_GLU66,SC_LYS292 REFERENCE16A reference value for a given contact, by default is 0=0.950000 WEIGHT16A weight value for a given contact, by default is 1=1.0 SWITCH16The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 66-292
  ATOMS17the atoms involved in each of the contacts you wish to calculate=SC_THR6,SC_ASP385 REFERENCE17A reference value for a given contact, by default is 0=0.950000 WEIGHT17A weight value for a given contact, by default is 1=1.0 SWITCH17The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 6-385
  ATOMS18the atoms involved in each of the contacts you wish to calculate=SC_ARG62,SC_THR128 REFERENCE18A reference value for a given contact, by default is 0=0.950000 WEIGHT18A weight value for a given contact, by default is 1=1.0 SWITCH18The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 62-128
  ATOMS19the atoms involved in each of the contacts you wish to calculate=SC_THR183,SC_LEU203 REFERENCE19A reference value for a given contact, by default is 0=0.950000 WEIGHT19A weight value for a given contact, by default is 1=1.0 SWITCH19The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 183-203
  ATOMS20the atoms involved in each of the contacts you wish to calculate=SC_HIS295,SC_THR298 REFERENCE20A reference value for a given contact, by default is 0=0.950000 WEIGHT20A weight value for a given contact, by default is 1=1.0 SWITCH20The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12}  # 295-298
  CMDIST calculate the distance with respect to the provided reference contact map
...

#  individual contact fractions (diagnostic) 
The CONTACTMAP action with label cmap_apo_specific calculates the following quantities: Quantity    Description  
cmap_apo_specific.contact By not using SUM or CMDIST each contact will be stored in a component
cmap_apo_specific.value the sum of all the switching function on all the distancess_holo_184_201: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ALA184 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ALA201 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 184-201
The COORDINATION action with label s_holo_184_201 calculates the following quantities: Quantity    Description  
s_holo_184_201.value the value of the coordinations_holo_188_197: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG188 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LEU197 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 188-197
The COORDINATION action with label s_holo_188_197 calculates the following quantities: Quantity    Description  
s_holo_188_197.value the value of the coordinations_holo_25_167: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG25 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_VAL167 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 25-167
The COORDINATION action with label s_holo_25_167 calculates the following quantities: Quantity    Description  
s_holo_25_167.value the value of the coordinations_holo_182_203: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_PRO182 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LEU203 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 182-203
The COORDINATION action with label s_holo_182_203 calculates the following quantities: Quantity    Description  
s_holo_182_203.value the value of the coordinations_holo_169_291: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG169 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_GLY291 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 169-291
The COORDINATION action with label s_holo_169_291 calculates the following quantities: Quantity    Description  
s_holo_169_291.value the value of the coordinations_holo_181_203: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLN181 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LEU203 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 181-203
The COORDINATION action with label s_holo_181_203 calculates the following quantities: Quantity    Description  
s_holo_181_203.value the value of the coordinations_holo_62_74: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG62 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_THR74 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 62-74
The COORDINATION action with label s_holo_62_74 calculates the following quantities: Quantity    Description  
s_holo_62_74.value the value of the coordinations_holo_126_291: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_SER126 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_GLY291 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 126-291
The COORDINATION action with label s_holo_126_291 calculates the following quantities: Quantity    Description  
s_holo_126_291.value the value of the coordinations_holo_128_140: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_THR128 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_CYS140 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 128-140
The COORDINATION action with label s_holo_128_140 calculates the following quantities: Quantity    Description  
s_holo_128_140.value the value of the coordinations_holo_130_284: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLN130 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LYS284 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 130-284
The COORDINATION action with label s_holo_130_284 calculates the following quantities: Quantity    Description  
s_holo_130_284.value the value of the coordinations_holo_241_248: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ILE241 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_GLN248 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 241-248
The COORDINATION action with label s_holo_241_248 calculates the following quantities: Quantity    Description  
s_holo_241_248.value the value of the coordinations_holo_178_207: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_PRO178 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ILE207 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 178-207
The COORDINATION action with label s_holo_178_207 calculates the following quantities: Quantity    Description  
s_holo_178_207.value the value of the coordinations_holo_293_296: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_LEU293 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_GLU296 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 293-296
The COORDINATION action with label s_holo_293_296 calculates the following quantities: Quantity    Description  
s_holo_293_296.value the value of the coordinations_holo_55_85: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_VAL55 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_GLN85 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 55-85
The COORDINATION action with label s_holo_55_85 calculates the following quantities: Quantity    Description  
s_holo_55_85.value the value of the coordinations_holo_130_131: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLN130 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_PRO131 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 130-131
The COORDINATION action with label s_holo_130_131 calculates the following quantities: Quantity    Description  
s_holo_130_131.value the value of the coordinations_holo_186_198: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_THR186 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_HIS198 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 186-198
The COORDINATION action with label s_holo_186_198 calculates the following quantities: Quantity    Description  
s_holo_186_198.value the value of the coordinations_holo_72_136: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLY72 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_THR136 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 72-136
The COORDINATION action with label s_holo_72_136 calculates the following quantities: Quantity    Description  
s_holo_72_136.value the value of the coordinations_holo_282_297: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG282 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ASP297 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 282-297
The COORDINATION action with label s_holo_282_297 calculates the following quantities: Quantity    Description  
s_holo_282_297.value the value of the coordinations_holo_47_52: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_TYR47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ARG52 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 47-52
The COORDINATION action with label s_holo_47_52 calculates the following quantities: Quantity    Description  
s_holo_47_52.value the value of the coordinations_holo_290_298: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ASP290 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_THR298 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 290-298
The COORDINATION action with label s_holo_290_298 calculates the following quantities: Quantity    Description  
s_holo_290_298.value the value of the coordinations_apo_189_197: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLN189 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LEU197 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 189-197
The COORDINATION action with label s_apo_189_197 calculates the following quantities: Quantity    Description  
s_apo_189_197.value the value of the coordinations_apo_187_199: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_THR187 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LEU199 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 187-199
The COORDINATION action with label s_apo_187_199 calculates the following quantities: Quantity    Description  
s_apo_187_199.value the value of the coordinations_apo_185_201: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLU185 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ALA201 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 185-201
The COORDINATION action with label s_apo_185_201 calculates the following quantities: Quantity    Description  
s_apo_185_201.value the value of the coordinations_apo_8_389: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_VAL8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_GLU389 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 8-389
The COORDINATION action with label s_apo_8_389 calculates the following quantities: Quantity    Description  
s_apo_8_389.value the value of the coordinations_apo_8_387: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_VAL8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_VAL387 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 8-387
The COORDINATION action with label s_apo_8_387 calculates the following quantities: Quantity    Description  
s_apo_8_387.value the value of the coordinations_apo_6_387: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_THR6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_VAL387 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 6-387
The COORDINATION action with label s_apo_6_387 calculates the following quantities: Quantity    Description  
s_apo_6_387.value the value of the coordinations_apo_10_389: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_LYS10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_GLU389 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 10-389
The COORDINATION action with label s_apo_10_389 calculates the following quantities: Quantity    Description  
s_apo_10_389.value the value of the coordinations_apo_64_139: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLY64 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ALA139 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 64-139
The COORDINATION action with label s_apo_64_139 calculates the following quantities: Quantity    Description  
s_apo_64_139.value the value of the coordinations_apo_10_391: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_LYS10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_PHE391 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 10-391
The COORDINATION action with label s_apo_10_391 calculates the following quantities: Quantity    Description  
s_apo_10_391.value the value of the coordinations_apo_169_297: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG169 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ASP297 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 169-297
The COORDINATION action with label s_apo_169_297 calculates the following quantities: Quantity    Description  
s_apo_169_297.value the value of the coordinations_apo_25_391: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG25 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_PHE391 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 25-391
The COORDINATION action with label s_apo_25_391 calculates the following quantities: Quantity    Description  
s_apo_25_391.value the value of the coordinations_apo_26_393: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ASP26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ARG393 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 26-393
The COORDINATION action with label s_apo_26_393 calculates the following quantities: Quantity    Description  
s_apo_26_393.value the value of the coordinations_apo_25_297: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG25 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ASP297 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 25-297
The COORDINATION action with label s_apo_25_297 calculates the following quantities: Quantity    Description  
s_apo_25_297.value the value of the coordinations_apo_294_396: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_LYS294 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LEU396 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 294-396
The COORDINATION action with label s_apo_294_396 calculates the following quantities: Quantity    Description  
s_apo_294_396.value the value of the coordinations_apo_296_394: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLU296 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_GLN394 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 296-394
The COORDINATION action with label s_apo_296_394 calculates the following quantities: Quantity    Description  
s_apo_296_394.value the value of the coordinations_apo_66_292: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_GLU66 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LYS292 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 66-292
The COORDINATION action with label s_apo_66_292 calculates the following quantities: Quantity    Description  
s_apo_66_292.value the value of the coordinations_apo_6_385: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_THR6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_ASP385 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 6-385
The COORDINATION action with label s_apo_6_385 calculates the following quantities: Quantity    Description  
s_apo_6_385.value the value of the coordinations_apo_62_128: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_ARG62 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_THR128 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 62-128
The COORDINATION action with label s_apo_62_128 calculates the following quantities: Quantity    Description  
s_apo_62_128.value the value of the coordinations_apo_183_203: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_THR183 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_LEU203 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 183-203
The COORDINATION action with label s_apo_183_203 calculates the following quantities: Quantity    Description  
s_apo_183_203.value the value of the coordinations_apo_295_298: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC_HIS295 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC_THR298 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.350859 D_0=0.0 NN=6 MM=12} NOPBC ignore the periodic boundary conditions when calculating distances  # 295-298

# --- End of included input --- 
#  twist proxy (needed for p_rmsd_twist_l0p1 + theta_rev axis) 
The COORDINATION action with label s_apo_295_298 calculates the following quantities: Quantity    Description  
s_apo_295_298.value the value of the coordinationgN1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=144,315,612,663,821,882,1396,1825,2356,2405,2622
The GROUP action with label gN1 calculates somethinggN2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=408,456,956,986,1195,1261,1292,2104,2236,2270,2697,2778,4635,4714
The GROUP action with label gN2 calculates somethinggC1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=3327,3367,3865,3887,3989,4016,5039,5103,5559,5612
The GROUP action with label gC1 calculates somethinggC2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2998,3036,3168,3204,3534,3564,3642,3694,4261,4286,5227,5284,5446,5485
The GROUP action with label gC2 calculates somethingN1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gN1 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label N1 calculates somethingN2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gN2 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label N2 calculates somethingC1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gC1 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label C1 calculates somethingC2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gC2 NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label C2 calculates somethinggN: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=63,70,84,108,124,144,166,188,198,211,223,237,244,266,285,299,315,336,355,362,384,408,420,440,456,468,485,504,516,535,551,565,577,593,605,612,628,644,663,679,693,705,720,741,760,782,797,821,845,861,882,898,912,931,945,956,966,986,1010,1031,1038,1062,1077,1089,1108,1120,1136,1155,1162,1181,1195,1215,1239,1261,1273,1292,1312,1328,1338,1352,1368,1385,1396,1418,1432,1444,1456,1468,1483,1495,1517,1541,1553,1572,1586,1610,1629,1646,1661,1685,1704,1723,1745,1767,1786,1793,1808,1825,1835,1858,1870,1890,1904,1924,1939,1960,1974,1986,2000,2021,2033,2044,2055,2071,2085,2104,2123,2135,2144,2156,2171,2183,2197,2204,2226,2236,2247,2254,2270,2282,2303,2318,2334,2356,2366,2386,2405,2415,2430,2444,2463,2478,2493,2515,2534,2551,2573,2597,2611,2622,2638,2662,2681,2697,2716,2740,2762,2778  # N-domain CA 5-172
The GROUP action with label gN calculates somethinggC: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2795,2816,2828,2840,2855,2881,2893,2902,2914,2933,2945,2959,2969,2984,2998,3012,3036,3053,3073,3092,3109,3120,3132,3156,3168,3187,3204,3223,3238,3248,3259,3278,3290,3312,3327,3346,3367,3388,3405,3412,3429,3441,3460,3471,3487,3501,3517,3534,3550,3564,3578,3592,3606,3620,3642,3656,3672,3694,3716,3735,3757,3776,3787,3803,3827,3844,3865,3875,3887,3906,3922,3941,3961,3975,3989,3999,4016,4037,4059,4077,4089,4105,4115,4132,4147,4162,4172,4184,4196,4210,4226,4238,4250,4261,4272,4286,4306,4317,4339,4355,4376,4390,4409,4425,4437,4457,4476,4486,4500,4514,4538,4553,4575,4599,4606,4625,4635,4654,4666,4673,4695,4714,4736,4753,4768,4780,4794,4808,4827,4837,4848,4859,4873,4892,4911,4935,4950,4957,4967,4981,5005,5020,5039,5058,5065,5084,5103,5119,5130,5151,5173,5189,5211,5227,5249,5268,5284,5300,5311,5335,5342,5349,5368,5387,5394,5406,5425,5435,5446,5457,5469,5485,5495,5511,5526,5547,5559,5579,5593,5612  # C-domain CA 173-352
The GROUP action with label gC calculates somethingNcom: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gN NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label Ncom calculates somethingCcom: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gC NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label Ccom calculates somethingtwist: TORSIONCalculate one or multiple torsional angles. More details VECTOR1You should use VECTORA instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=N1,N2 AXIStwo atoms that define an axis=Ncom,Ccom VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=C1,C2 NOPBC ignore the periodic boundary conditions when calculating distances

#  RMSD / path CV 
The TORSION action with label twist calculates the following quantities: Quantity    Description  
twist.value the TORSION involving these atomsr_active_sq:   RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../refs/holo_ndomain_align_cdomain_structured_ca.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL SQUARED  This should be set if you want MSD instead of RMSD 
The RMSD action with label r_active_sq calculates the following quantities: Quantity    Description  
r_active_sq.value the RMSD distance between the instantaneous structure and the reference structure/s that were inputr_inactive_sq: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../refs/apo_ndomain_align_cdomain_structured_ca.pdb  TYPE the manner in which RMSD alignment is performed=OPTIMAL SQUARED  This should be set if you want MSD instead of RMSD 
The RMSD action with label r_inactive_sq calculates the following quantities: Quantity    Description  
r_inactive_sq.value the RMSD distance between the instantaneous structure and the reference structure/s that were inputp_rmsd_twist_l0p1: FUNCPATHMSDThis function calculates path collective variables. More details ARGthe labels of the values from which the function is calculated=r_inactive_sq,r_active_sq LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=0.1

#  theta_rev (uses Ncom/Ccom; anchor from R62+R76 SC; FL midpoint 69/70 CA) 
The FUNCPATHMSD action with label p_rmsd_twist_l0p1 calculates the following quantities: Quantity    Description  
p_rmsd_twist_l0p1.s the position on the path
p_rmsd_twist_l0p1.z the distance from the pathR62_sc: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=988,991,994,997,999-1000,1003
The GROUP action with label R62_sc calculates somethingR76_sc: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1217,1220,1223,1226,1228-1229,1232
The GROUP action with label R76_sc calculates somethingCOM_R62_R76: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=R62_sc,R76_sc NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label COM_R62_R76 calculates somethingFL_M: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1108,1120
The GROUP action with label FL_M calculates somethingCOM_FL_M: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=FL_M NOPBC ignore the periodic boundary conditions when calculating distances
The COM action with label COM_FL_M calculates somethingtheta_rev: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=Ncom,Ccom,COM_R62_R76,COM_FL_M NOPBC ignore the periodic boundary conditions when calculating distances
The ANGLE action with label theta_rev calculates the following quantities: Quantity    Description  
theta_rev.value the ANGLE involving these atomstheta_rev_deg: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=theta_rev FUNCthe function you wish to evaluate=x*180/pi PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The MATHEVAL action with label theta_rev_deg calculates the following quantities: Quantity    Description  
theta_rev_deg.value an arbitrary functionuwall_z: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p_rmsd_twist_l0p1.z ATthe positions of the wall=2 KAPPAthe force constant for the wall=10000.0 EXP the powers for the walls=2

#  OPES: path + ionic lock  (all replicas) 
The UPPER_WALLS action with label uwall_z calculates the following quantities: Quantity    Description  
uwall_z.bias the instantaneous value of the bias potential
uwall_z.force2 the instantaneous value of the squared force due to this bias potentialOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes_main
  ARGthe labels of the scalars on which the bias will act (a vector must have a single element, e=p_rmsd_twist_l0p1.s
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.01
  FILE a file in which the list of all deposited kernels is stored=Kernels_main.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels_main
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels_main
  PACEthe frequency for kernel deposition=50000 BARRIERthe free energy barrier to be overcome=50
... OPES_METAD_EXPLORE

#  OPES: polar core  (replicas 1-4) 
The OPES_METAD_EXPLORE action with label opes_main calculates the following quantities: Quantity    Description  
opes_main.bias the instantaneous value of the bias potential
opes_main.rct estimate of c(t)
opes_main.zed estimate of Z_n
opes_main.neff effective sample size
opes_main.nker total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes_polcore
  ARGthe labels of the scalars on which the bias will act (a vector must have a single element, e=R169_D290,R169_D26
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1,0.1
  FILE a file in which the list of all deposited kernels is stored=Kernels_polcore.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels_polcore
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels_polcore
  PACEthe frequency for kernel deposition=10000 BARRIERthe free energy barrier to be overcome=5
... OPES_METAD_EXPLORE

#  OPES: theta_rev  (replicas 1-4) 
The OPES_METAD_EXPLORE action with label opes_polcore calculates the following quantities: Quantity    Description  
opes_polcore.bias the instantaneous value of the bias potential
opes_polcore.rct estimate of c(t)
opes_polcore.zed estimate of Z_n
opes_polcore.neff effective sample size
opes_polcore.nker total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes_theta
  ARGthe labels of the scalars on which the bias will act (a vector must have a single element, e=theta_rev,dist_R62_D67,dist_R76_D69
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1,0.1,0.1
  FILE a file in which the list of all deposited kernels is stored=Kernels_theta.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels_theta
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels_theta
  PACEthe frequency for kernel deposition=10000 BARRIERthe free energy barrier to be overcome=10
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes_theta calculates the following quantities: Quantity    Description  
opes_theta.bias the instantaneous value of the bias potential
opes_theta.rct estimate of c(t)
opes_theta.zed estimate of Z_n
opes_theta.neff effective sample size
opes_theta.nker total number of compressed kernels used to represent the biasPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR FMT the format that should be used to output real numbers=%12.6f
Quantity	Description
d_FL_LR.value	the DISTANCE between this pair of atoms
Quantity	Description
d_FL_ML.value	the DISTANCE between this pair of atoms
Quantity	Description
d_ML_LR.value	the DISTANCE between this pair of atoms
Quantity	Description
K77_E313.value	the DISTANCE between this pair of atoms
Quantity	Description
R169_D290.value	the DISTANCE between this pair of atoms
Quantity	Description
R169_D26.value	the DISTANCE between this pair of atoms
Quantity	Description
R25_D297.value	the DISTANCE between this pair of atoms
Quantity	Description
D29_K170.value	the DISTANCE between this pair of atoms
Quantity	Description
dist_R62_D67.value	the DISTANCE between this pair of atoms
Quantity	Description
dist_R76_D69.value	the DISTANCE between this pair of atoms
Quantity	Description
K10_D390.value	the DISTANCE between this pair of atoms
Quantity	Description
K10_E389.value	the DISTANCE between this pair of atoms
Quantity	Description
R393_D26.value	the DISTANCE between this pair of atoms
Quantity	Description
R393_D297.value	the DISTANCE between this pair of atoms
Quantity	Description
R25_V167.value	the DISTANCE between this pair of atoms
Quantity	Description
R169_G291.value	the DISTANCE between this pair of atoms
Quantity	Description
Q189_L197.value	the DISTANCE between this pair of atoms
Quantity	Description
R169_D297.value	the DISTANCE between this pair of atoms
Quantity	Description
Q394_E296.value	the DISTANCE between this pair of atoms
Quantity	Description
H295_T298.value	the DISTANCE between this pair of atoms
PLUMED-NEST

The public repository of the PLUMED consortium
