Project ID: plumID:19.083
Source: Reaction_discovery/1.H2_NO/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
RESTART
Activate restart. More details
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
N:
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
=1,3 O:
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
=2,4 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
=5,6,7,8
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
nn:
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
=N
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.5 NN=6 MM=8}
MEAN
calculate the mean of all the quantities
oo:
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
=O
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
MEAN
calculate the mean of all the quantities
no:
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
=N
SPECIESB
this keyword is used for colvars such as the coordination number
=O
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} on:
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
=O
SPECIESB
this keyword is used for colvars such as the coordination number
=N
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} nh:
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
=N
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=1.4 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02} hn:
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
=N
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02} oh:
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
=O
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=1.4 NN=6 MM=8}
MIN
calculate the minimum value
={BETA=20.0}
MAX
calculate the maximum value
={BETA=0.02} ho:
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
=O
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL D_0=0.0 R_0=1.4 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
=1.00
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
=nn.mean
COEFFICIENTS
the coefficients of the arguments in your function
=1.0734
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
=oo.mean
COEFFICIENTS
the coefficients of the arguments in your function
=1.6782
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
=no.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.7097
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
=no.min
COEFFICIENTS
the coefficients of the arguments in your function
=0.7637
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
=on.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.7121
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
=on.min
COEFFICIENTS
the coefficients of the arguments in your function
=0.7643
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
=nh.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.9618
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
=nh.min
COEFFICIENTS
the coefficients of the arguments in your function
=1.1010
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
=hn.max
COEFFICIENTS
the coefficients of the arguments in your function
=1.3052
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
=hn.min
COEFFICIENTS
the coefficients of the arguments in your function
=2.5949
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
=oh.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.3617
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
=oh.min
COEFFICIENTS
the coefficients of the arguments in your function
=0.4227
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
=ho.max
COEFFICIENTS
the coefficients of the arguments in your function
=0.6276
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
=ho.min
COEFFICIENTS
the coefficients of the arguments in your function
=0.8866
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
#the following are 32,33,34 svd14:
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
=0.0,-0.02114,0.00334,-0.23391,-0.64088,0.21637,0.69767,0.00113,-0.00213,-0.00001,0.00025,0.00206,-0.00739,-0.00457,-0.02124
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
=0.0,-0.39547,0.06121,-0.20744,0.60671,-0.11341,0.47938,0.02201,-0.03897,-0.00129,0.00439,0.03726,-0.13914,-0.08409,-0.39524
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO svd12:
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
=0.0,-0.40711,0.06514,-0.17925,0.61216,-0.15080,0.50432,0.02309,-0.04043,-0.00128,0.00438,-0.02035,-0.27076,-0.03965,-0.26189
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
dNN:
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
=N
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=N
MAX
calculate the maximum value
={BETA=0.02}
NOPBC
ignore the periodic boundary conditions when calculating distances
dNH:
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
=N
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H
MAX
calculate the maximum value
={BETA=0.02}
NOPBC
ignore the periodic boundary conditions when calculating distances
dOO:
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
=O
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=O
MAX
calculate the maximum value
={BETA=0.02}
NOPBC
ignore the periodic boundary conditions when calculating distances
wallNN:
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
=dNN.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 wallNH:
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
=dNH.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 wallNaN:
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
=dOO.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
=svd13
SIGMA
the widths of the Gaussian hills
=0.05
HEIGHT
the heights of the Gaussian hills
=3.0
PACE
the frequency for hill addition
=100
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint ... 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