Project ID: plumID:20.021
Source: plumed_K200.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=./ref.pdba file in pdb format containing a reference structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-661,661-500:-1,1300-1475,1475-662:-1the atoms that make up a molecule that you wish to alignCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-2067a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=755,755,755,755,755,755,755,755,758,758,758,758,758,758,758,758,758,758,758,758,758,758,758,758,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,764,764,764,764,764,764,764,764,764,764,764,764First list of atomsGROUPB=717,808,830,832,1245,1247,1251,1288,278,808,811,813,817,827,830,832,836,1245,1247,1288,1298,1310,1359,1362,278,808,811,813,817,827,830,832,836,1245,1247,1288,1298,1301,1308,1310,1359,1362,278,830,832,836,1247,1288,1298,1359,1362,1365,1366,1367 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-2067:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-2067the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=22.68the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-2070a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=808,808,808,808,808,808,808,808,808,808,808,808,808,808,808,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817First list of atomsGROUPB=755,758,760,863,876,878,1074,1080,1126,1128,1132,1135,1247,1251,1310,436,758,760,878,1074,1076,1080,1126,1128,1135,1145,1148,1150,1154,1247,1251,1308,1310,436,758,760,1074,1080,1126,1128,1132,1145,1148,1150,1154,1245,1247,1251,1298,1301,1306,1308,1310,274,436,758,760,887,890,892,896,1074,1076,1080,1128,1145,1154,1301,1306,1308,1310 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-2070:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-2070the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=31.95the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-2087a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1090,1090,1090,1090,1093,1093,1093,1093,1093,1093,1093,1095,1095,1095,1095,1095,1095,1099,1099,1099,1099,1099,1099First list of atomsGROUPB=429,497,501,1040,429,492,495,497,501,1164,1170,427,429,492,495,497,501,429,492,495,497,501,1170 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-2087:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-2087the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=20.93the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-2096a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1242,1242,1242,1242,1242,1242,1242,1242,1242,1242,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251First list of atomsGROUPB=700,703,745,1148,1150,1197,1200,1201,1202,1288,703,745,755,758,760,813,1132,1145,1148,1150,1197,1200,1201,1202,1288,1298,703,745,755,758,760,764,808,811,813,1150,1202,1288,1298,745,755,808,811,813,1126,1128,1132,1135,1145,1148,1150,1197,1200,1201,1202 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-2096:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-2096the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=44.55the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-2099a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1288,1288,1288,1288,1288,1288,1288,1288,1288,1288,1288,1288First list of atomsGROUPB=700,703,711,755,758,760,764,1242,1245,1247,1337,1362 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-2099:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-2099the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=.720the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-1048a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=141,141,141,141,144,144,144,146,146,146First list of atomsGROUPB=194,197,198,199,197,198,199,197,198,199 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-1048:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-1048the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=3.60the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-1049a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=160,160,160,160,160,160,160,163,163,163,163,163,163,165,165,165,165,165,169,169,169,169,169,169,169First list of atomsGROUPB=208,211,213,777,780,781,782,211,213,777,780,781,782,774,777,780,781,782,211,213,774,777,780,781,782 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-1049:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-1049the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=7.75the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-1055a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=250,250,250,250,250,250,250,250,250,250,250,253,253,253,253,253,253,253,253,253,253,253,253,253,255,255,255,255,255,255,255,255,255,255,259,259,259,259,259,259,259,259,259,259,259,259,259,259,259,259First list of atomsGROUPB=208,211,217,299,302,316,827,830,832,836,896,208,217,310,316,827,830,836,887,890,896,906,909,912,299,310,316,887,890,896,906,909,912,915,208,211,217,316,827,830,832,836,887,890,892,896,906,909,912,915 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-1055:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-1055the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=41.50the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-1067a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=427,427,427,427,427,427,427,427,427,427,427,429,429,429,429,429,429,429,429,429,429,429,429,429,433,433,433,433,433,433,433,433,433,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436First list of atomsGROUPB=492,495,501,1076,1095,1145,1148,1154,1304,1306,1308,492,495,501,1074,1076,1090,1093,1095,1099,1145,1148,1154,1306,383,386,392,1076,1154,1304,1306,1308,1310,383,386,388,392,811,813,817,892,896,1074,1076,1080,1145,1148,1154,1301,1302,1304,1306,1308,1310 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-1067:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-1067the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=12.42the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-1047a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=131,131First list of atomsGROUPB=179,182 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-1047:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-1047the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=.42the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-1054a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=239,239,239,239,239,239,239,239,239,242,242,242,242,242,242,242First list of atomsGROUPB=288,291,299,302,1431,1432,1433,1435,1437,291,302,1431,1432,1433,1435,1437 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-1054:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-1054the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=3.84the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-1062a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=351,351,351,351,351,354,354,354,354,357,357,357,357,357,358,358,358First list of atomsGROUPB=324,327,328,329,402,327,328,329,402,402,467,469,470,473,469,470,473 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-1062:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-1062the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=5.27the position of the restraintCOORDINATION...Calculate coordination numbers. More detailsPAIRPair only 1st element of the 1st group with 1st element in the second, etcNOPBCignore the periodic boundary conditions when calculating distancesLABEL=pv-1065a label for the action so that its output can be referenced in the input to other actionsSWITCH={RATIONAL R_0=0.65 D_MAX=1.3}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=402,402,402,402,402,402,402,402,402,402,402,402First list of atomsGROUPB=351,354,357,446,458,461,464,467,469,470,473,482 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
rpv-1065:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-1065the arguments on which the bias is actingSLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=200specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=.60the position of the restraint
stat:STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More detailsARG=pv-2067,pv-2070,pv-2087,pv-2096,pv-2099,pv-1048,pv-1049,pv-1055,pv-1067,pv-1047,pv-1054,pv-1062,pv-1065the input for this action is the scalar output from one or more other actionsPARAMETERS=22.68,31.95,20.93,44.55,0.72,3.60,7.75,41.50,12.42,0.42,3.84,5.27,0.60the parameters of the arguments in your functionPrint quantities to a file. More detailsARG=statthe input for this action is the scalar output from one or more other actionsFILE=STATthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=pv-2067,pv-2070,pv-2087,pv-2096,pv-2099,pv-1048,pv-1049,pv-1055,pv-1067,pv-1047,pv-1054,pv-1062,pv-1065the input for this action is the scalar output from one or more other actionsFILE=COORDINATIONthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=rpv-2067.bias,rpv-2070.bias,rpv-2087.bias,rpv-2096.bias,rpv-2099.bias,rpv-1048.bias,rpv-1049.bias,rpv-1055.bias,rpv-1067.bias,rpv-1047.bias,rpv-1054.bias,rpv-1062.bias,rpv-1065.biasthe input for this action is the scalar output from one or more other actionsFILE=RESTRAINTSthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be output