Project ID: plumID:20.030
Source: plumed2.dat
Originally used with PLUMED version: 2.6
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
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MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=ref.pdb WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-1571 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-76 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1305,1308,1309,1310,1305,1308,1309,1309,1305,1308,1309,1305,1308,1309,1310,1305,1308,1309,1310,1308,1309,1310,1308,1309,1310,1308,1309,1310,1309,1309,1310,1310,1310,1310,1305,1305,1308,1308,1308,1308,1309,1309,1309,1309,1310,1310,1310,1310, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=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, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-76 ARGthe values input to this function=allpv-76 COEFFICIENTS the coefficients of the arguments in your function=0.0208333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-76: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-76 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.28 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-39 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=684,684,684,684,684,684,686,686,690,690,690, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=743,757,760,1347,1390,1393,1390,1393,1347,1390,1393, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-39 ARGthe values input to this function=allpv-39 COEFFICIENTS the coefficients of the arguments in your function=0.0909091 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-39: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-39 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.42 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-78 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1338,1338,1338,1347,1347,1338,1341,1343,1347,1341,1343,1338,1338,1338,1341,1341,1347,1347, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=594,596,600,684,690,1284,1284,1284,1284,1287,1287,1295,1390,1393,1390,1393,1390,1393, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-78 ARGthe values input to this function=allpv-78 COEFFICIENTS the coefficients of the arguments in your function=0.0555556 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-78: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-78 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.49 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-81 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1390,1393,1390,1393,1390,1393,1390,1393,1390,1393,1393,1393,1393,1390,1393,1393,1390,1393,1390,1393,1390,1393,1390,1390, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=684,684,686,686,690,690,743,743,745,745,757,760,762,824,824,1319,1338,1338,1341,1341,1347,1347,1435,1441, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-81 ARGthe values input to this function=allpv-81 COEFFICIENTS the coefficients of the arguments in your function=0.0416667 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-81: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-81 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.51 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-29 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=517,519,514,514,514,514,514,514,517,517,517,517,517,517,519,519,519,519,519,519,523,523,523,523, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=375,375,450,569,1360,1362,1366,1401,569,1360,1401,1416,1419,1421,1360,1401,1416,1419,1421,1425,1401,1404,1416,1482, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-29 ARGthe values input to this function=allpv-29 COEFFICIENTS the coefficients of the arguments in your function=0.0416667 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-29: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-29 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.74 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-47 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=824,824,824,824,824,824,824,824,824,824,824,824, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=745,757,905,1319,1322,1324,1376,1379,1390,1393,1435,1441, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-47 ARGthe values input to this function=allpv-47 COEFFICIENTS the coefficients of the arguments in your function=0.0833333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-47: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-47 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.80 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-71 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1241,1239,1241,1239,1241,1239,1241,1239,1241,1241,1236,1239,1241, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=591,594,594,596,596,600,600,1157,1157,1159,1295,1295,1295, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-71 ARGthe values input to this function=allpv-71 COEFFICIENTS the coefficients of the arguments in your function=0.0769231 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-71: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-71 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.86 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-58 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1015,1017,1015,1017,1024,1015,1017,1021,1024,1017,1015,1017,1021,1024,1024,1024,1024,1015,1015,1021, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=258,258,256,256,450,453,453,453,453,455,459,459,459,459,469,472,475,1051,1057,1057, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-58 ARGthe values input to this function=allpv-58 COEFFICIENTS the coefficients of the arguments in your function=0.05 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-58: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-58 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.90 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-86 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1482,1473,1473, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=523,1416,1419, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-86 ARGthe values input to this function=allpv-86 COEFFICIENTS the coefficients of the arguments in your function=0.333333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-86: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-86 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=0.99 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-26 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=453,455,459,453,455,459,453,455,459,453,455,459,455,455,455,450,450,453,455,450,453,455,459,450,450,450,453,453,453,453,453,453,455,455,455,455,459,459,459,459,459, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=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, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-26 ARGthe values input to this function=allpv-26 COEFFICIENTS the coefficients of the arguments in your function=0.0243902 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-26: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-26 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=1.00 COORDINATIONCalculate coordination numbers. More details ... PAIR Pair only 1st element of the 1st group with 1st element in the second, etc NOPBC ignore the periodic boundary conditions when calculating distances LABELa label for the action so that its output can be referenced in the input to other actions=allpv-79 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=0.75 D_MAX=1.5 NN=18 MM=23} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 GROUPAFirst list of atoms=1357,1360,1357,1360,1362,1366,1366,1357,1360,1366,1357,1360,1362,1366,1360,1366,1366,1362,1366,1360,1362,1366,1360,1360,1362,1362,1362,1357,1360,1357,1360,1362,1357,1357,1357,1357,1360,1357, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=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, ... COORDINATION
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=pv-79 ARGthe values input to this function=allpv-79 COEFFICIENTS the coefficients of the arguments in your function=0.0263158 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO rpv-79: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=pv-79 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50000. ATthe position of the restraint=1.00 stat: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=pv-76,pv-39,pv-78,pv-81,pv-29,pv-47,pv-71,pv-58,pv-86,pv-26,pv-79, PARAMETERSthe parameters of the arguments in your function=0.28,0.42,0.49,0.51,0.74,0.80,0.86,0.90,0.99,1.00,1.00, PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=stat.* FILEthe name of the file on which to output these quantities=STAT STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=pv-76,pv-39,pv-78,pv-81,pv-29,pv-47,pv-71,pv-58,pv-86,pv-26,pv-79, FILEthe name of the file on which to output these quantities=COORDINATION STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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.bias, FILEthe name of the file on which to output these quantities=RESTRAINTS STRIDE the frequency with which the quantities of interest should be output=500