**Project ID:** plumID:20.030

**Source:** plumed1.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=1-1571the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-76SWITCH={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23}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=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1305,1308,1309,1310,1305,1308,1309,1309,1305,1308,1309,1305,1308,1309,1310,1305,1308,1309,1310,1308,1309,1310,1308,1309,1310,1308,1309,1310,1309,1309,1310,1310,1310,1310,1305,1305,1308,1308,1308,1308,1309,1309,1309,1309,1310,1310,1310,1310First list of atomsGROUPB=246,246,246,246,249,249,249,258,256,256,256,258,258,258,258,266,266,266,266,269,269,269,281,281,281,283,283,283,293,299,893,896,899,902,1357,1381,1357,1379,1380,1381,1357,1360,1379,1381,1376,1379,1380,1381 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-76ARG=the input for this action is the scalar output from one or more other actionsallpv-76COEFFICIENTS=0.0208333the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionrpv-76:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-76SLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=20000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=0.28the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-39SWITCH={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23}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=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=684,684,684,684,684,684,686,686,690,690,690First list of atomsGROUPB=743,757,760,1347,1390,1393,1390,1393,1347,1390,1393 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-39ARG=the input for this action is the scalar output from one or more other actionsallpv-39COEFFICIENTS=0.0909091the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionrpv-39:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-39SLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=20000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=0.42the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-78SWITCH={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23}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=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1338,1338,1338,1347,1347,1338,1341,1343,1347,1341,1343,1338,1338,1338,1341,1341,1347,1347First list of atomsGROUPB=594,596,600,684,690,1284,1284,1284,1284,1287,1287,1295,1390,1393,1390,1393,1390,1393 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-78ARG=the input for this action is the scalar output from one or more other actionsallpv-78COEFFICIENTS=0.0555556the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionrpv-78:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-78SLOPE=0specifies that the restraint is linear and what the values of the force constants on each of the variables areKAPPA=20000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=0.49the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-81NLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1390,1393,1390,1393,1390,1393,1390,1393,1390,1393,1393,1393,1393,1390,1393,1393,1390,1393,1390,1393,1390,1393,1390,1390First list of atomsGROUPB=684,684,686,686,690,690,743,743,745,745,757,760,762,824,824,1319,1338,1338,1341,1341,1347,1347,1435,1441 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-81ARG=the input for this action is the scalar output from one or more other actionsallpv-81COEFFICIENTS=0.0416667the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionrpv-81:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-81AT=0.51the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-29NLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=517,519,514,514,514,514,514,514,517,517,517,517,517,517,519,519,519,519,519,519,523,523,523,523First list of atomsGROUPB=375,375,450,569,1360,1362,1366,1401,569,1360,1401,1416,1419,1421,1360,1401,1416,1419,1421,1425,1401,1404,1416,1482 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-29ARG=the input for this action is the scalar output from one or more other actionsallpv-29COEFFICIENTS=0.0416667the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionrpv-29:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-29AT=0.74the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-47NLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=824,824,824,824,824,824,824,824,824,824,824,824First list of atomsGROUPB=745,757,905,1319,1322,1324,1376,1379,1390,1393,1435,1441 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-47ARG=the input for this action is the scalar output from one or more other actionsallpv-47COEFFICIENTS=0.0833333the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionrpv-47:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-47AT=0.80the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-71NLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1241,1239,1241,1239,1241,1239,1241,1239,1241,1241,1236,1239,1241First list of atomsGROUPB=591,594,594,596,596,600,600,1157,1157,1159,1295,1295,1295 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-71ARG=the input for this action is the scalar output from one or more other actionsallpv-71COEFFICIENTS=0.0769231the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionrpv-71:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-71AT=0.86the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-58NLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1015,1017,1015,1017,1024,1015,1017,1021,1024,1017,1015,1017,1021,1024,1024,1024,1024,1015,1015,1021First list of atomsGROUPB=258,258,256,256,450,453,453,453,453,455,459,459,459,459,469,472,475,1051,1057,1057 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-58ARG=the input for this action is the scalar output from one or more other actionsallpv-58COEFFICIENTS=0.05the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionrpv-58:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-58AT=0.90the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-86NLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1482,1473,1473First list of atomsGROUPB=523,1416,1419 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-86ARG=the input for this action is the scalar output from one or more other actionsallpv-86COEFFICIENTS=0.333333the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionrpv-86:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-86AT=0.99the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-26NLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=453,455,459,453,455,459,453,455,459,453,455,459,455,455,455,450,450,453,455,450,453,455,459,450,450,450,453,453,453,453,453,453,455,455,455,455,459,459,459,459,459First list of atomsGROUPB=246,246,246,249,249,249,258,258,258,256,256,256,293,295,299,366,372,372,372,375,375,375,375,514,980,1024,980,1015,1017,1021,1024,1366,980,1017,1362,1366,980,1015,1017,1021,1024 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-26ARG=the input for this action is the scalar output from one or more other actionsallpv-26COEFFICIENTS=0.0243902the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionrpv-26:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-26AT=1.00the 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=a label for the action so that its output can be referenced in the input to other actionsallpv-79NLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.6The cutoff for the neighbor listNL_STRIDE=20The frequency with which we are updating the atoms in the neighbor listGROUPA=1357,1360,1357,1360,1362,1366,1366,1357,1360,1366,1357,1360,1362,1366,1360,1366,1366,1362,1366,1360,1362,1366,1360,1360,1362,1362,1362,1357,1360,1357,1360,1362,1357,1357,1357,1357,1360,1357First list of atomsGROUPB=246,246,249,249,249,249,254,256,256,256,258,258,258,258,295,295,453,455,455,514,514,514,517,519,533,536,538,594,594,596,596,596,600,1305,1308,1309,1309,1401 ... COORDINATIONSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)COMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionspv-79ARG=the input for this action is the scalar output from one or more other actionsallpv-79COEFFICIENTS=0.0263158the coefficients of the arguments in your functionif the output of your function is periodic then you should specify the periodicity of the functionrpv-79:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the input for this action is the scalar output from one or more other actionspv-79AT=1.00the position of the restraintstat:STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More detailsARG=the input for this action is the scalar output from one or more other actionspv-76,pv-39,pv-78,pv-81,pv-29,pv-47,pv-71,pv-58,pv-86,pv-26,pv-79PARAMETERS=0.28,0.42,0.49,0.51,0.74,0.80,0.86,0.90,0.99,1.00,1.00the parameters of the arguments in your functionPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsstatFILE=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=the input for this action is the scalar output from one or more other actionspv-76,pv-39,pv-78,pv-81,pv-29,pv-47,pv-71,pv-58,pv-86,pv-26,pv-79FILE=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=the input for this action is the scalar output from one or more other actionsrpv-76.bias,rpv-39.bias,rpv-78.bias,rpv-81.bias,rpv-29.bias,rpv-47.bias,rpv-71.bias,rpv-58.bias,rpv-86.bias,rpv-26.bias,rpv-79.biasFILE=RESTRAINTSthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be output