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

Click on the labels of the actions for more information on what each action computes
tested onv2.8
tested onmaster
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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 for this action is the scalar output from one or more other actions
=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 input for this action is the scalar output from one or more other actions
=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
=1000
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
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