Project ID: plumID:20.030
Source: plumed0.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=allpv-76a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=pv-76a label for the action so that its output can be referenced in the input to other actionsARG=allpv-76the input to this functionCOEFFICIENTS=0.0208333the coefficients of the arguments in your functionPERIODIC=NO rpv-76:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-76the 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=1000specifies 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=allpv-39a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=pv-39a label for the action so that its output can be referenced in the input to other actionsARG=allpv-39the input to this functionCOEFFICIENTS=0.0909091the coefficients of the arguments in your functionPERIODIC=NO rpv-39:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-39the 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=1000specifies 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=allpv-78a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=pv-78a label for the action so that its output can be referenced in the input to other actionsARG=allpv-78the input to this functionCOEFFICIENTS=0.0555556the coefficients of the arguments in your functionPERIODIC=NO rpv-78:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-78the 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=1000specifies 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=allpv-81a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=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=pv-81a label for the action so that its output can be referenced in the input to other actionsARG=allpv-81the input to this functionCOEFFICIENTS=0.0416667the coefficients of the arguments in your functionPERIODIC=NO rpv-81:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-81the 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=1000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=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=allpv-29a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=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=pv-29a label for the action so that its output can be referenced in the input to other actionsARG=allpv-29the input to this functionCOEFFICIENTS=0.0416667the coefficients of the arguments in your functionPERIODIC=NO rpv-29:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-29the 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=1000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=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=allpv-47a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=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=pv-47a label for the action so that its output can be referenced in the input to other actionsARG=allpv-47the input to this functionCOEFFICIENTS=0.0833333the coefficients of the arguments in your functionPERIODIC=NO rpv-47:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-47the 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=1000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=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=allpv-71a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=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=pv-71a label for the action so that its output can be referenced in the input to other actionsARG=allpv-71the input to this functionCOEFFICIENTS=0.0769231the coefficients of the arguments in your functionPERIODIC=NO rpv-71:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-71the 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=1000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=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=allpv-58a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=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=pv-58a label for the action so that its output can be referenced in the input to other actionsARG=allpv-58the input to this functionCOEFFICIENTS=0.05the coefficients of the arguments in your functionPERIODIC=NO rpv-58:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-58the 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=1000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=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=allpv-86a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=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=pv-86a label for the action so that its output can be referenced in the input to other actionsARG=allpv-86the input to this functionCOEFFICIENTS=0.333333the coefficients of the arguments in your functionPERIODIC=NO rpv-86:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-86the 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=1000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=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=allpv-26a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=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=pv-26a label for the action so that its output can be referenced in the input to other actionsARG=allpv-26the input to this functionCOEFFICIENTS=0.0243902the coefficients of the arguments in your functionPERIODIC=NO rpv-26:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-26the 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=1000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=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=allpv-79a label for the action so that its output can be referenced in the input to other actionsSWITCH={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=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=pv-79a label for the action so that its output can be referenced in the input to other actionsARG=allpv-79the input to this functionCOEFFICIENTS=0.0263158the coefficients of the arguments in your functionPERIODIC=NO rpv-79:if the output of your function is periodic then you should specify the periodicity of the functionRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=pv-79the 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=1000specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=1.00the 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-76,pv-39,pv-78,pv-81,pv-29,pv-47,pv-71,pv-58,pv-86,pv-26,pv-79the input for this action is the scalar output from one or more other actionsPARAMETERS=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=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-76,pv-39,pv-78,pv-81,pv-29,pv-47,pv-71,pv-58,pv-86,pv-26,pv-79the 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-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.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