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
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=Cmumd.cpp

The LOAD action with label  calculates somethinggra: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1-9152:1 
The GROUP action with label gra calculates somethingsod: GROUPDefine 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 ATOMSthe 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: GROUPDefine 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 ATOMSthe 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: GROUPDefine 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 ATOMSthe 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: CMUMDThis 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: CMUMDThis 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: CMUMDThis 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

RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=nsod ATthe 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 LABELa 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 potentialRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=nchl ATthe 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 LABELa 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 potentialPRINTPrint quantities to a file. More details ...
ARGthe labels of the values that you would like to print to the file=nsod,nchl,nwat,resna.bias,rescl.bias
 STRIDE the frequency with which the quantities of interest should be output=50
 FILEthe name of the file on which to output these quantities=COLVAR
... PRINT