Project ID: plumID:20.021
Source: plumed_K200.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 onv2.9
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
=1-661,661-500:-1,1300-1475,1475-662:-1
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
=pv-2067
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=755,755,755,755,755,755,755,755,758,758,758,758,758,758,758,758,758,758,758,758,758,758,758,758,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,760,764,764,764,764,764,764,764,764,764,764,764,764
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=717,808,830,832,1245,1247,1251,1288,278,808,811,813,817,827,830,832,836,1245,1247,1288,1298,1310,1359,1362,278,808,811,813,817,827,830,832,836,1245,1247,1288,1298,1301,1308,1310,1359,1362,278,830,832,836,1247,1288,1298,1359,1362,1365,1366,1367 ... COORDINATION
rpv-2067:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-2067
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
=200
AT
the position of the restraint
=22.68
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
=pv-2070
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=808,808,808,808,808,808,808,808,808,808,808,808,808,808,808,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,811,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,813,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817,817
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=755,758,760,863,876,878,1074,1080,1126,1128,1132,1135,1247,1251,1310,436,758,760,878,1074,1076,1080,1126,1128,1135,1145,1148,1150,1154,1247,1251,1308,1310,436,758,760,1074,1080,1126,1128,1132,1145,1148,1150,1154,1245,1247,1251,1298,1301,1306,1308,1310,274,436,758,760,887,890,892,896,1074,1076,1080,1128,1145,1154,1301,1306,1308,1310 ... COORDINATION
rpv-2070:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-2070
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
=200
AT
the position of the restraint
=31.95
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
=pv-2087
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=1090,1090,1090,1090,1093,1093,1093,1093,1093,1093,1093,1095,1095,1095,1095,1095,1095,1099,1099,1099,1099,1099,1099
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=429,497,501,1040,429,492,495,497,501,1164,1170,427,429,492,495,497,501,429,492,495,497,501,1170 ... COORDINATION
rpv-2087:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-2087
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
=200
AT
the position of the restraint
=20.93
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
=pv-2096
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=1242,1242,1242,1242,1242,1242,1242,1242,1242,1242,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1245,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1247,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251,1251
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=700,703,745,1148,1150,1197,1200,1201,1202,1288,703,745,755,758,760,813,1132,1145,1148,1150,1197,1200,1201,1202,1288,1298,703,745,755,758,760,764,808,811,813,1150,1202,1288,1298,745,755,808,811,813,1126,1128,1132,1135,1145,1148,1150,1197,1200,1201,1202 ... COORDINATION
rpv-2096:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-2096
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
=200
AT
the position of the restraint
=44.55
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
=pv-2099
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=1288,1288,1288,1288,1288,1288,1288,1288,1288,1288,1288,1288
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=700,703,711,755,758,760,764,1242,1245,1247,1337,1362 ... COORDINATION
rpv-2099:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-2099
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
=200
AT
the position of the restraint
=.720
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
=pv-1048
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=141,141,141,141,144,144,144,146,146,146
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=194,197,198,199,197,198,199,197,198,199 ... COORDINATION
rpv-1048:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-1048
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
=200
AT
the position of the restraint
=3.60
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
=pv-1049
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=160,160,160,160,160,160,160,163,163,163,163,163,163,165,165,165,165,165,169,169,169,169,169,169,169
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=208,211,213,777,780,781,782,211,213,777,780,781,782,774,777,780,781,782,211,213,774,777,780,781,782 ... COORDINATION
rpv-1049:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-1049
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
=200
AT
the position of the restraint
=7.75
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
=pv-1055
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=250,250,250,250,250,250,250,250,250,250,250,253,253,253,253,253,253,253,253,253,253,253,253,253,255,255,255,255,255,255,255,255,255,255,259,259,259,259,259,259,259,259,259,259,259,259,259,259,259,259
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=208,211,217,299,302,316,827,830,832,836,896,208,217,310,316,827,830,836,887,890,896,906,909,912,299,310,316,887,890,896,906,909,912,915,208,211,217,316,827,830,832,836,887,890,892,896,906,909,912,915 ... COORDINATION
rpv-1055:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-1055
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
=200
AT
the position of the restraint
=41.50
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
=pv-1067
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=427,427,427,427,427,427,427,427,427,427,427,429,429,429,429,429,429,429,429,429,429,429,429,429,433,433,433,433,433,433,433,433,433,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436,436
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=492,495,501,1076,1095,1145,1148,1154,1304,1306,1308,492,495,501,1074,1076,1090,1093,1095,1099,1145,1148,1154,1306,383,386,392,1076,1154,1304,1306,1308,1310,383,386,388,392,811,813,817,892,896,1074,1076,1080,1145,1148,1154,1301,1302,1304,1306,1308,1310 ... COORDINATION
rpv-1067:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-1067
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
=200
AT
the position of the restraint
=12.42
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
=pv-1047
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=131,131
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=179,182 ... COORDINATION
rpv-1047:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-1047
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
=200
AT
the position of the restraint
=.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
=pv-1054
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=239,239,239,239,239,239,239,239,239,242,242,242,242,242,242,242
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=288,291,299,302,1431,1432,1433,1435,1437,291,302,1431,1432,1433,1435,1437 ... COORDINATION
rpv-1054:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-1054
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
=200
AT
the position of the restraint
=3.84
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
=pv-1062
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=351,351,351,351,351,354,354,354,354,357,357,357,357,357,358,358,358
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=324,327,328,329,402,327,328,329,402,402,467,469,470,473,469,470,473 ... COORDINATION
rpv-1062:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-1062
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
=200
AT
the position of the restraint
=5.27
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
=pv-1065
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.65 D_MAX=1.3}
NLIST
Use a neighbor list to speed up the calculation
NL_CUTOFF
The cutoff for the neighbor list
=1.4
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
GROUPA
First list of atoms
=402,402,402,402,402,402,402,402,402,402,402,402
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=351,354,357,446,458,461,464,467,469,470,473,482 ... COORDINATION
rpv-1065:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=pv-1065
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
=200
AT
the position of the restraint
=.60
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-2067,pv-2070,pv-2087,pv-2096,pv-2099,pv-1048,pv-1049,pv-1055,pv-1067,pv-1047,pv-1054,pv-1062,pv-1065
PARAMETERS
the parameters of the arguments in your function
=22.68,31.95,20.93,44.55,0.72,3.60,7.75,41.50,12.42,0.42,3.84,5.27,0.60
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-2067,pv-2070,pv-2087,pv-2096,pv-2099,pv-1048,pv-1049,pv-1055,pv-1067,pv-1047,pv-1054,pv-1062,pv-1065
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-2067.bias,rpv-2070.bias,rpv-2087.bias,rpv-2096.bias,rpv-2099.bias,rpv-1048.bias,rpv-1049.bias,rpv-1055.bias,rpv-1067.bias,rpv-1047.bias,rpv-1054.bias,rpv-1062.bias,rpv-1065.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