PLUMED-NEST

Project ID: plumID:21.049
Source: 1ad_multi/plumed.0.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

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../PathCV.cpp
The LOAD action with label  calculates something
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=ps 
ENERGY
the units of energy
=kcal/mol

phi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
The TORSION action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomswphi: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values input to this function
=phi 
COEFFICIENTS
 the coefficients of the arguments in your function
=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 wphi calculates the following quantities:
 Quantity   
 Description  
wphi.value
a linear compbination
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
=wphi 
AT
the positions of the wall
=-2.7 
KAPPA
the force constant for the wall
=1000.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=philwall
The LOWER_WALLS action with label philwall calculates the following quantities:
 Quantity   
 Description  
philwall.bias
the instantaneous value of the bias potential
philwall.force2
the instantaneous value of the squared force due to this bias potential
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
=wphi 
AT
the positions of the wall
=2.7  
KAPPA
the force constant for the wall
=1000.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=phiuwall

The UPPER_WALLS action with label phiuwall calculates the following quantities:
 Quantity   
 Description  
phiuwall.bias
the instantaneous value of the bias potential
phiuwall.force2
the instantaneous value of the squared force due to this bias potentialpsi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17
The TORSION action with label psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomswpsi: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values input to this function
=psi 
COEFFICIENTS
 the coefficients of the arguments in your function
=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 wpsi calculates the following quantities:
 Quantity   
 Description  
wpsi.value
a linear compbination
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
=wpsi 
AT
the positions of the wall
=-2.7 
KAPPA
the force constant for the wall
=1000.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=psilwall
The LOWER_WALLS action with label psilwall calculates the following quantities:
 Quantity   
 Description  
psilwall.bias
the instantaneous value of the bias potential
psilwall.force2
the instantaneous value of the squared force due to this bias potential
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
=wpsi 
AT
the positions of the wall
=2.7  
KAPPA
the force constant for the wall
=1000.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=psiuwall

The UPPER_WALLS action with label psiuwall calculates the following quantities:
 Quantity   
 Description  
psiuwall.bias
the instantaneous value of the bias potential
psiuwall.force2
the instantaneous value of the squared force due to this bias potentialce6: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=1
The CONSTANT action with label ce6 calculates the following quantities:
 Quantity   
 Description  
ce6.value
the constant value that was read from the plumed inputce7: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=1

The CONSTANT action with label ce7 calculates the following quantities:
 Quantity   
 Description  
ce7.value
the constant value that was read from the plumed inputens6: 
ENSEMBLE
Calculates the replica averaging of a collective variable over multiple replicas. More details
 
ARG
the labels of the values from which the function is calculated
=phi,psi,ce6 
MOMENT
the moment you want to calculate in alternative to the mean or the variance
=2 
CENTRAL
 calculate a central moment instead of a standard moment
 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
The ENSEMBLE action with label ens6 calculates the following quantities:
 Quantity   
 Description  
ens6..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsens7: 
ENSEMBLE
Calculates the replica averaging of a collective variable over multiple replicas. More details
 
ARG
the labels of the values from which the function is calculated
=phi,psi,ce7 
MOMENT
the moment you want to calculate in alternative to the mean or the variance
=2 
CENTRAL
 calculate a central moment instead of a standard moment
 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy

The ENSEMBLE action with label ens7 calculates the following quantities:
 Quantity   
 Description  
ens7..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for details
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
=ens6.phi_m,ens6.psi_m 
AT
the positions of the wall
=0.0,0.0 
KAPPA
the force constant for the wall
=0.0,0.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=act6
The LOWER_WALLS action with label act6 calculates the following quantities:
 Quantity   
 Description  
act6.bias
the instantaneous value of the bias potential
act6.force2
the instantaneous value of the squared force due to this bias potential
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
=ens7.phi_m,ens7.psi_m 
AT
the positions of the wall
=0.0,0.0 
KAPPA
the force constant for the wall
=0.0,0.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=act7

The LOWER_WALLS action with label act7 calculates the following quantities:
 Quantity   
 Description  
act7.bias
the instantaneous value of the bias potential
act7.force2
the instantaneous value of the squared force due to this bias potential
PATHCV
This action is not part of PLUMED and was included by using a LOAD command More details
 LABEL=pcv ARG=phi,psi GENPATH=20,20,20,-1.4,1.2,1.1,-0.8 FIXED=21,40 HALFLIFE=1000 PACE=250 WALKERS_RSTRIDE=250 WALKERS_ID=0 WALKERS_N=4 WALKERS_DIR OUTFILE=0_PATH

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
=pcv.z 
AT
the positions of the wall
=0.0  
KAPPA
the force constant for the wall
=70.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=tube
The UPPER_WALLS action with label tube calculates the following quantities:
 Quantity   
 Description  
tube.bias
the instantaneous value of the bias potential
tube.force2
the instantaneous value of the squared force due to this bias potential
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
=pcv.s 
AT
the positions of the wall
=-0.4 
KAPPA
the force constant for the wall
=50.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwall
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potential
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
=pcv.s 
AT
the positions of the wall
=1.4  
KAPPA
the force constant for the wall
=50.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potential
METAD
Used to performed metadynamics on one or more collective variables. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad 
ARG
the labels of the scalars on which the bias will act
=pcv.s 
HEIGHT
the heights of the Gaussian hills
=0.02 
SIGMA
the widths of the Gaussian hills
=0.05 
INTERVAL
one dimensional lower and upper limits, outside the limits the system will not feel the biasing force
=-0.4,1.4 
GRID_MIN
the lower bounds for the grid
=-1.0 
GRID_MAX
the upper bounds for the grid
=2.0 
PACE
the frequency for hill addition
=250 
WALKERS_RSTRIDE
stride for reading hills files
=250 
WALKERS_ID
walker id
=0 
WALKERS_N
number of walkers
=3 
WALKERS_DIR
shared directory with the hills files from all the walkers
 
FILE
 a file in which the list of added hills is stored
=0_HILLS

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
ARG
the labels of the values that you would like to print to the file
=phi,psi,pcv.s,pcv.z,metad.bias,tube.bias,philwall.bias,phiuwall.bias,psilwall.bias,psiuwall.bias,lwall.bias,uwall.bias 
FILE
the name of the file on which to output these quantities
=./0_COLVAR