Project ID: plumID:19.083
Source: Reaction_discovery/2.ICl/step1/B/plumed.dat
Originally used with PLUMED version: 2.5
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
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
H:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=1,2 I:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=3,5 Cl:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=4,6
hh:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIES
this keyword is used for colvars such as coordination number
=H
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8}
MEAN
calculate the mean of all the quantities
II:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIES
this keyword is used for colvars such as coordination number
=I
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=3.0 NN=6 MM=8}
MEAN
calculate the mean of all the quantities
ClCl:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIES
this keyword is used for colvars such as coordination number
=Cl
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=2.3 NN=6 MM=8}
MEAN
calculate the mean of all the quantities
HCl:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=H
SPECIESB
this keyword is used for colvars such as the coordination number
=Cl
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02} ClH:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=Cl
SPECIESB
this keyword is used for colvars such as the coordination number
=H
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02} HI:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=H
SPECIESB
this keyword is used for colvars such as the coordination number
=I
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.9 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02} IH:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=I
SPECIESB
this keyword is used for colvars such as the coordination number
=H
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.9 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02} ICl:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=I
SPECIESB
this keyword is used for colvars such as the coordination number
=Cl
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=2.6 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02} ClI:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=Cl
SPECIESB
this keyword is used for colvars such as the coordination number
=I
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=2.6 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02}
d1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=hh.mean
COEFFICIENTS
the coefficients of the arguments in your function
=1.0232
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d2:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=II.mean
COEFFICIENTS
the coefficients of the arguments in your function
=1.1790
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d3:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=ClCl.mean
COEFFICIENTS
the coefficients of the arguments in your function
=2.1364
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d4:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=HCl.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.7082
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d5:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=HCl.min
COEFFICIENTS
the coefficients of the arguments in your function
=0.8116
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d6:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=ClH.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.6879
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d7:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=ClH.min
COEFFICIENTS
the coefficients of the arguments in your function
=0.7994
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d8:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=HI.max
COEFFICIENTS
the coefficients of the arguments in your function
=1.1615
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d9:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=HI.min
COEFFICIENTS
the coefficients of the arguments in your function
=1.7905
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d10:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=IH.max
COEFFICIENTS
the coefficients of the arguments in your function
=1.2714
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d11:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=IH.min
COEFFICIENTS
the coefficients of the arguments in your function
=1.6849
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d12:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=ICl.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.8310
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d13:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=ICl.min
COEFFICIENTS
the coefficients of the arguments in your function
=0.9355
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d14:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=ClI.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.8257
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO d15:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=ClI.min
COEFFICIENTS
the coefficients of the arguments in your function
=0.9352
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
sdg1full:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.6688,-0.0250,-0.2889,-0.3031,-0.5252,0.2230,-0.1102,-0.0069,0.0331,-0.0102,-0.0103,0.1540,-0.0335,0.0968,0.0583
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
svd13m1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=-0.4446,0.0049,0.0288,0.1219,0.0686,0.0886,0.0323,0.1243,0.0676,-0.0530,-0.0781,0.4969,0.3439,-0.4511,-0.4189
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO svd13m2:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=-0.0450,0.0427,0.2969,-0.4559,0.4762,-0.0061,0.1473,-0.3869,-0.1632,0.2848,0.2102,-0.0487,0.2557,-0.2622,-0.1160
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO svd11m1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=-0.8075,0.0186,0.2521,0.1816,0.2349,0.0562,0.3967,0.0364,-0.0429,0.0242,-0.0034,-0.1252,-0.0373,-0.1007,-0.0662
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO svd11m2:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.1102,0.1135,0.5696,-0.1055,0.2089,-0.1612,0.2692,-0.2625,0.2177,-0.1559,-0.0388,-0.4719,0.2804,-0.2171,0.0822
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO svd9m1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.7820,-0.0074,-0.0974,-0.2334,0.0800,-0.1052,-0.1291,-0.2370,0.3061,-0.0213,-0.1431,-0.0234,0.2626,-0.0026,0.2235
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO svd9m2:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.0079,-0.2227,0.0969,-0.0597,-0.3591,0.1200,-0.5246,0.4716,-0.4417,0.1350,0.2572,0.1127,-0.0455,0.0354,0.0322
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO sdg1filter075:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=-0.4916,0.0056,0.0378,0.2220,0.1772,0.0,-0.0576,-0.0072,0.0050,0.0775,0.0,0.4842,0.2992,-0.4425,-0.3835
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO sdg2filter075:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.0269,-0.0375,-0.2456,0.3938,-0.3926,0.0,-0.1366,0.0201,-0.0019,0.0464,0.0,-0.1701,-0.5095,0.4204,0.3766
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO sdg1filter095:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.7429,-0.0276,-0.3225,0.0,-0.4192,-0.0218,-0.3448,-0.0248,0.0316,0.0,-0.0045,0.1832,-0.0276,0.0958,0.0550
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO sdg1filter090:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.7026,-0.0342,-0.3478,0.0,-0.3629,0.0,-0.3840,-0.0031,0.0186,0.0,-0.0052,0.2806,0.1303,0.0,-0.0945
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO svd13:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.7435,-0.0278,-0.3230,0.0052,-0.4295,-0.0315,-0.3276,-0.0540,0.0093,0.0297,0.0162,0.1870,-0.0130,0.0911,0.0412
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO svd11:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15
COEFFICIENTS
the coefficients of the arguments in your function
=0.7739,-0.0297,-0.3295,-0.1430,-0.2591,-0.0257,-0.3954,-0.0026,0.0093,0.0020,-0.0007,0.1858,-0.0170,0.0995,0.0471
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
dHCl:
DISTANCES
Calculate the distances between multiple piars of atoms More details
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=Cl
MAX
calculate the maximum value
={BETA=0.02}
NOPBC
ignore the periodic boundary conditions when calculating distances
dHI:
DISTANCES
Calculate the distances between multiple piars of atoms More details
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=I
MAX
calculate the maximum value
={BETA=0.02}
NOPBC
ignore the periodic boundary conditions when calculating distances
dICl:
DISTANCES
Calculate the distances between multiple piars of atoms More details
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=I
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=Cl
MAX
calculate the maximum value
={BETA=0.02}
NOPBC
ignore the periodic boundary conditions when calculating distances
wallHCl:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=dHCl.max
AT
the positions of the wall
=9.0
KAPPA
the force constant for the wall
=200.0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1 wallHI:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=dHI.max
AT
the positions of the wall
=9.0
KAPPA
the force constant for the wall
=200.0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1 wallICl:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=dICl.max
AT
the positions of the wall
=9.0
KAPPA
the force constant for the wall
=200.0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1
METAD
Used to performed metadynamics on one or more collective variables. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=svd13m1,svd13m2
SIGMA
the widths of the Gaussian hills
=0.05,0.05
HEIGHT
the heights of the Gaussian hills
=1.5
PACE
the frequency for hill addition
=100
BIASFACTOR
use well tempered metadynamics and use this bias factor
=60
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=400.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint
WALKERS_N
number of walkers
=3
WALKERS_ID
walker id
=1
WALKERS_DIR
shared directory with the hills files from all the walkers
WALKERS_RSTRIDE
stride for reading hills files
=50 ... METAD
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
STRIDE
the frequency with which the quantities of interest should be output
=20
FILE
the name of the file on which to output these quantities
=COLVAR
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
STRIDE
the frequency with which all the open files should be flushed
=20
ENDPLUMED
Terminate plumed input. More details