PLUMED-NEST

Project ID: plumID:20.024
Source: Hydrobromination/known_propene/plumed.dat
Originally used with PLUMED version: 2.7
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../../GAMBES.cpp
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=fs

d1:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,11 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d1 calculates a scalar quantityd2:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,1 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d2 calculates a scalar quantityd3:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,2 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d3 calculates a scalar quantityd4:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,2 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d4 calculates a scalar quantityd5:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=10,1 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d5 calculates a scalar quantityene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates a scalar quantitys1: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5 
COEFFICIENTS
 the coefficients of the arguments in your function
=-0.523,0.726,0.401,-0.029,-0.193 
POWERS
 the powers to which you are raising each of the arguments in your function
=1,1,1,1,1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The COMBINE action with label s1 calculates a scalar quantitys2: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.573,-0.339,-0.183,-0.636,-0.345 
POWERS
 the powers to which you are raising each of the arguments in your function
=1,1,1,1,1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The COMBINE action with label s2 calculates a scalar quantity
GAMBES
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
  ARG=d1 
  NSTATES=2
  FILENAME=gaussian
  PACE=500
  LABEL=ext
  BIAS_CUTOFF
  CUTOFF=100
  LAMBDA=0.1 
  TEMPERATURE=300
... GAMBES


#..............................WALLS.................................................
uwall: UPPER_WALLS ARG=d1,d2,d3,d4,d5 AT=3.0,3.0,3.0,3.0,3.0 KAPPA=150.0,150.0,150.0,150.0,150.0  #eps=1, exp=2, offset=0 : 
default
This action is not part of PLUMED and was included by using a LOAD command More details
 values

H1: 
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
=3,4
H2: 
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
=7,8,9
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
=11
C_end: 
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
=1,5
C_mid: 
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
Br: 
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
=10
Ce1: 
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
Ce2: 
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
H_all: 
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
=3,4,6,7,8,9,11

dCe1H1: 
DISTANCES
Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=Ce1 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H1 
HIGHEST
this flag allows you to recover the highest of these variables
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCES action with label dCe1H1 calculates the following quantities:
 Quantity   
 Description  
dCe1H1.highest
the highest of the quantities calculated by this actiondCe2H2: 
DISTANCES
Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=Ce2 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H2 
HIGHEST
this flag allows you to recover the highest of these variables
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCES action with label dCe2H2 calculates the following quantities:
 Quantity   
 Description  
dCe2H2.highest
the highest of the quantities calculated by this actiondCmH1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,6 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dCmH1 calculates a scalar quantitydHH: 
DISTANCES
Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H_all 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H_all 
MIN
calculate the minimum value
={BETA=20} 
NOPBC
 ignore the periodic boundary conditions when calculating distances

The DISTANCES action with label dHH calculates the following quantities:
 Quantity   
 Description  
dHH.min
the minimum valued13: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,3 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d13 calculates a scalar quantityd14: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,4 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d14 calculates a scalar quantitywallCe1H1: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d13,d14 
AT
the positions of the wall
=1.4,1.4 
KAPPA
the force constant for the wall
=150.0,150.0 
EXP
 the powers for the walls
=2,2 
EPS
 the values for s_i in the expression for a wall
=1.0,1.0 
OFFSET
 the offset for the start of the wall
=0.2,0.2

The UPPER_WALLS action with label wallCe1H1 calculates the following quantities:
 Quantity   
 Description  
wallCe1H1.bias
the instantaneous value of the bias potential
wallCe1H1.force2
the instantaneous value of the squared force due to this bias potentiald57: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,7 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d57 calculates a scalar quantityd58: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,8 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d58 calculates a scalar quantityd59: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,9 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d59 calculates a scalar quantitywallCe2H2: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d57,d58,d59 
AT
the positions of the wall
=1.4,1.4,1.4 
KAPPA
the force constant for the wall
=150.0,150.0,150.0 
EXP
 the powers for the walls
=2,2,2 
EPS
 the values for s_i in the expression for a wall
=1.0,1.0,1.0 
OFFSET
 the offset for the start of the wall
=0.2,0.2,0.2
The UPPER_WALLS action with label wallCe2H2 calculates the following quantities:
 Quantity   
 Description  
wallCe2H2.bias
the instantaneous value of the bias potential
wallCe2H2.force2
the instantaneous value of the squared force due to this bias potentialwallCmH1: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dCmH1 
AT
the positions of the wall
=1.4 
KAPPA
the force constant for the wall
=150.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1.0 
OFFSET
 the offset for the start of the wall
=0.2
The UPPER_WALLS action with label wallCmH1 calculates the following quantities:
 Quantity   
 Description  
wallCmH1.bias
the instantaneous value of the bias potential
wallCmH1.force2
the instantaneous value of the squared force due to this bias potentialwallHH: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dHH 
AT
the positions of the wall
=1.4 
KAPPA
the force constant for the wall
=150.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1.0 #OFFSET=1.3
##################################################


The LOWER_WALLS action with label wallHH calculates the following quantities:
 Quantity   
 Description  
wallHH.bias
the instantaneous value of the bias potential
wallHH.force2
the instantaneous value of the squared force due to this bias potential
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
=10 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%8.4f
#PRINT ARG=ext.probability.0,ext.probability.1,ext.probability.2 STRIDE=10 FILE=GAMBES FMT=%8.10f