PLUMED-NEST

Project ID: plumID:23.027
Source: plumed.dat
Originally used with PLUMED version: 2.5.1
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

# Plumed script to perform CmuMD simulations
# Aaron R. Finney and Matteo Salvalaglio
# Properties of aqueous electrolyte solutions at carbon electrodes: 
# effects of concentration and surface charge on solution structure, ion clustering and thermodynamics in the electric double layer
# June 2023
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=Cmumd.cpp

The LOAD action with label  calculates somethinggra: 
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
=1-9152:1 
The GROUP action with label gra calculates somethingsod: 
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
=43320-43737,46622-47039,49828-50245,53118-53535
The GROUP action with label sod calculates somethingchl: 
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
=43738-44155,47040-47457,50246-50663,53536-53953
The GROUP action with label chl calculates somethingwat: 
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
=9153-43319,44156-46621,47458-49827,50664-53117

The GROUP action with label wat calculates somethingnwat: 
CMUMD
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUP=wat NSV=3 DCR=0.1953 CRSIZE=0.1172 WF=0.0001 NINT=1.0 NZ=372
nsod: 
CMUMD
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUP=sod NSV=1 FIXED=0.5 DCR=0.1953 CRSIZE=0.1172 WF=0.0001 NINT=0.1 NZ=372
nchl: 
CMUMD
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUP=chl NSV=1 FIXED=0.5 DCR=0.1953 CRSIZE=0.1172 WF=0.0001 NINT=0.1 NZ=372

RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=nsod 
AT
the position of the restraint
=3.0110 
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=20000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=resna
The RESTRAINT action with label resna calculates the following quantities:
 Quantity   
 Description  
resna.bias
the instantaneous value of the bias potential
resna.force2
the instantaneous value of the squared force due to this bias potential
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=nchl 
AT
the position of the restraint
=3.0110 
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=20000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rescl
#RESTRAINT ARG=n_water AT=29.5 KAPPA=20.0 LABEL=wres

The RESTRAINT action with label rescl calculates the following quantities:
 Quantity   
 Description  
rescl.bias
the instantaneous value of the bias potential
rescl.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
=nsod,nchl,nwat,resna.bias,rescl.bias
 
STRIDE
 the frequency with which the quantities of interest should be output
=50
 
FILE
the name of the file on which to output these quantities
=COLVAR
... PRINT