PLUMED-NEST

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

Click on the labels of the actions for more information on what each action computes

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=ref.pdb
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-1571

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-76
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First 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
GROUPB
Second 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

The COORDINATION action with label allpv-76 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-76  
ARG
the input to this function
=allpv-76 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0208333 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-76: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.28

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-39
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=684,684,684,684,684,684,686,686,690,690,690
GROUPB
Second 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

The COORDINATION action with label allpv-39 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-39  
ARG
the input to this function
=allpv-39 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0909091 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-39: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.42

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-78
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=1338,1338,1338,1347,1347,1338,1341,1343,1347,1341,1343,1338,1338,1338,1341,1341,1347,1347
GROUPB
Second 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

The COORDINATION action with label allpv-78 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-78  
ARG
the input to this function
=allpv-78 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0555556 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-78: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.49

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-81
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First 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
GROUPB
Second 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

The COORDINATION action with label allpv-81 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-81  
ARG
the input to this function
=allpv-81 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0416667 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-81: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.51

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-29
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First 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
GROUPB
Second 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

The COORDINATION action with label allpv-29 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-29  
ARG
the input to this function
=allpv-29 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0416667 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-29: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.74

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-47
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=824,824,824,824,824,824,824,824,824,824,824,824
GROUPB
Second 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

The COORDINATION action with label allpv-47 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-47  
ARG
the input to this function
=allpv-47 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0833333 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-47: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.80

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-71
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=1241,1239,1241,1239,1241,1239,1241,1239,1241,1241,1236,1239,1241
GROUPB
Second 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

The COORDINATION action with label allpv-71 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-71  
ARG
the input to this function
=allpv-71 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0769231 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-71: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.86

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-58
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=1015,1017,1015,1017,1024,1015,1017,1021,1024,1017,1015,1017,1021,1024,1024,1024,1024,1015,1015,1021
GROUPB
Second 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

The COORDINATION action with label allpv-58 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-58  
ARG
the input to this function
=allpv-58 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.05 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-58: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.90

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-86
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=1482,1473,1473
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=523,1416,1419
... COORDINATION

The COORDINATION action with label allpv-86 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-86  
ARG
the input to this function
=allpv-86 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.333333 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-86: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=0.99

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-26
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First 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
GROUPB
Second 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

The COORDINATION action with label allpv-26 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-26  
ARG
the input to this function
=allpv-26 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0243902 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-26: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=1.00

COORDINATION
Calculate 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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=allpv-79
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.75 D_MAX=1.5 NN=18 MM=23} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.6 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First 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
GROUPB
Second 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

The COORDINATION action with label allpv-79 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pv-79  
ARG
the input to this function
=allpv-79 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.0263158 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rpv-79: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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
=20000 
AT
the position of the restraint
=1.00

stat: 
STATS
Calculates statistical properties of a set of collective variables with respect to a set of reference values. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=pv-76,pv-39,pv-78,pv-81,pv-29,pv-47,pv-71,pv-58,pv-86,pv-26,pv-79 
PARAMETERS
the 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
The STATS action with label stat calculates the following quantities:
 Quantity   
 Description  
stat.sqdevsum
the sum of the squared deviations between arguments and parameters
stat.corr
the correlation between arguments and parameters
stat.slope
the slope of a linear fit between arguments and parameters
stat.intercept
the intercept of a linear fit between arguments and parameters
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=stat 
FILE
the name of the file on which to output these quantities
=STAT 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=pv-76,pv-39,pv-78,pv-81,pv-29,pv-47,pv-71,pv-58,pv-86,pv-26,pv-79 
FILE
the name of the file on which to output these quantities
=COORDINATION 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=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 
FILE
the name of the file on which to output these quantities
=RESTRAINTS 
STRIDE
 the frequency with which the quantities of interest should be output
=500