PLUMED-NEST

Project ID: plumID:21.049
Source: 3ad_cycle/plumed.6.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 atomsphic: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15 
COSINE
 calculate cosine instead of dihedral
The TORSION action with label phic calculates the following quantities:
 Quantity   
 Description  
phic.value
the TORSION involving these atomsphis: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=phi 
FUNC
the function you wish to evaluate
=sin(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The CUSTOM action with label phis calculates the following quantities:
 Quantity   
 Description  
phis.value
an arbitrary functionpsi: 
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 atomspsic: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17 
COSINE
 calculate cosine instead of dihedral
The TORSION action with label psic calculates the following quantities:
 Quantity   
 Description  
psic.value
the TORSION involving these atomspsis: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=psi 
FUNC
the function you wish to evaluate
=sin(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The CUSTOM action with label psis calculates the following quantities:
 Quantity   
 Description  
psis.value
an arbitrary function
PATHCV
This action is not part of PLUMED and was included by using a LOAD command More details
 LABEL=pcv ARG=phic,phis,psic,psis INFILE=in_cycle.input HALFLIFE=1000 PACE=250 WALKERS_RSTRIDE=250 WALKERS_ID=6 WALKERS_N=8 WALKERS_DIR

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
=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
=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 potentialc: 
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 c calculates the following quantities:
 Quantity   
 Description  
c.value
the constant value that was read from the plumed inputs: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values input to this function
=pcv.s,c 
COEFFICIENTS
 the coefficients of the arguments in your function
=2.,1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-1,1

The COMBINE action with label s calculates the following quantities:
 Quantity   
 Description  
s.value
a linear compbination
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
=s 
HEIGHT
the heights of the Gaussian hills
=0.08 
SIGMA
the widths of the Gaussian hills
=0.05 
PACE
the frequency for hill addition
=250 
WALKERS_RSTRIDE
stride for reading hills files
=250 
WALKERS_ID
walker id
=6 
WALKERS_N
number of walkers
=7 
WALKERS_DIR
shared directory with the hills files from all the walkers

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
=phic,phis,psic,psis,phi,psi,s,pcv.s,pcv.z,metad.bias,tube.bias 
FILE
the name of the file on which to output these quantities
=./COLVAR