Project ID: plumID:20.012
Source: COMet_Path/plumed.dat
Originally used with PLUMED version: 2.4.2
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 onv2.8
tested onmaster
tested on master
# Plumed file generated by the COMet script

#LOAD FILE=FuncPathGeneral.cpp # Now part of Plumed, not necessary to load it
# The file containing the CV definitions
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
FILE
file to be included
=cv_definitions.dat

path:
FUNCPATHGENERAL
This function calculates path collective variables (PCVs) using an arbitrary combination of collective variables. More details
ARG
the input for this action is the scalar output from one or more other actions
=pp.proj,pp.ext,d1,d2,d3,d4
COEFFICIENTS
Coefficients to be assigned to the CVs
=9.3101e-02,2.4712e-01,2.5745e-02,1.2017e-01,7.4306e-02,1.2492e-01
REFERENCE
Colvar file needed to provide the CV milestones
=COLVAR_PATH
LAMBDA
Lambda parameter required for smoothing
=7.4143e+02
# The file containing the CV restraints #INCLUDE FILE=restraints.dat
# Funnel s_cent:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=3.0 beta_cent:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=1.5 wall_width:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=1.2 wall_buffer:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=0.15
lwall:
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
=pp.proj
AT
the positions of the wall
=0.0
KAPPA
the force constant for the wall
=2000.0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1 uwall:
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
=pp.proj
AT
the positions of the wall
=4.5
KAPPA
the force constant for the wall
=2000.0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1
MATHEVAL
An alias to the ef CUSTOM function. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall_center
ARG
the input for this action is the scalar output from one or more other actions
=pp.proj,s_cent,beta_cent,wall_width,wall_buffer
VAR
the names to give each of the arguments in the function
=s,sc,b,h,f
FUNC
the function you wish to evaluate
=h*(1./(1.+exp(b*(s-sc))))+f
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
scaling:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=1.0 spring:
CONSTANT
Return one or more constant quantities with or without derivatives. More details
VALUES
The values of the constants
=1000.0
MATHEVAL
An alias to the ef CUSTOM function. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wall_bias
ARG
the input for this action is the scalar output from one or more other actions
=pp.ext,spring,wall_center,scaling
VAR
the names to give each of the arguments in the function
=z,k,zc,sf
FUNC
the function you wish to evaluate
=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ... MATHEVAL
finalbias:
BIASVALUE
Takes the value of one variable and use it as a bias More details
ARG
the input for this action is the scalar output from one or more other actions
=wall_bias
#zwall: UPPER_WALLS ARG=path.z AT=0.1 KAPPA=1000000
# Metadynamics
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 input for this action is the scalar output from one or more other actions
=path.s,path.z
SIGMA
the widths of the Gaussian hills
=0.15,0.0004
HEIGHT
the heights of the Gaussian hills
=2.0
PACE
the frequency for hill addition
=1000
FILE
a file in which the list of added hills is stored
=HILLS
BIASFACTOR
use well tempered metadynamics and use this bias factor
=12.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
GRID_MIN
the lower bounds for the grid
=0.95,-0.02
GRID_MAX
the upper bounds for the grid
=16.05,0.20
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.05,0.0002
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... 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
=1000
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