PLUMED-NEST

Project ID: plumID:20.024
Source: Hydrobromination/static_bias/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

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

s1: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=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
s2: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=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

GAMBES
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
  ARG=d1,d2,d3,d4,d5
  NSTATES=3
  FILENAME=gdist_n
  PACE=500
  LABEL=ext
  BIAS_CUTOFF
  CUTOFF=150
  LAMBDA=0.01 
  TEMPERATURE=300
  STATIC_BIAS
  STATIC_FACTORS=1,4000,1.0006
... GAMBES

uwall: 
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
=d1,d2,d3,d4,d5 
AT
the positions of the wall
=3.0,3.0,3.0,3.0,3.0 
KAPPA
the force constant for the wall
=150.0,150.0,150.0,150.0,150.0  

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 multiple piars of atoms 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
dCe2H2: 
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
=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
dCmH1: 
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 multiple piars of atoms 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

d13: 
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 arguments on which the bias is acting
=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

d57: 
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 arguments on which the bias is acting
=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
wallCmH1: 
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
=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
wallHH: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=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


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
=1 
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