**Project ID:** plumID:21.035

**Source:** CmuMD-NaCl/rough-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

LOADLoads a library, possibly defining new actions. More detailsFILE=Cmumd.cppfile to be loaded

# Define the groupsnaslab: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 detailsATOMS=1-1921the numerical indexes for the set of atoms in the groupclslab: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 detailsATOMS=1922-3842the numerical indexes for the set of atoms in the groupncslab: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 detailsATOMS=1-3842the numerical indexes for the set of atoms in the groupwatoxy:ATOMS=3843-45297:3the numerical indexes for the set of atoms in the groupnasoln:ATOMS=1-1921,45300-46971the numerical indexes for the set of atoms in the groupclsoln:ATOMS=1922-3842,46972-48643the numerical indexes for the set of atoms in the groupncsoln:ATOMS=1-3842,45300-48643the numerical indexes for the set of atoms in the group

# Middle of the slab #p0: FIXEDATOM AT=2.88992,2.88992,8.51019p0:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.88992,2.88992,8.65coordinates of the virtual atom

# Restrain the slabp1:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=1.965,2.154,8.214 # 535coordinates of the virtual atomp2:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.692,2.153,8.212 # 547coordinates of the virtual atomp3:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=1.969,3.892,8.211 # 655coordinates of the virtual atomp4:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.687,3.880,8.227 # 667coordinates of the virtual atomp5:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=1.959,2.147,8.794 # 935coordinates of the virtual atomp6:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.699,2.147,8.811 # 947coordinates of the virtual atomp7:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=1.963,3.889,8.796 #1055coordinates of the virtual atomp8:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=3.710,3.904,8.806 #1067coordinates of the virtual atomd1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp1,535d2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp2,547d3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp3,655d4:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp4,667d5:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp5,935d6:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp6,947d7:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp7,1055d8:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenp8,1067slabrest:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the arguments on which the bias is actingd1,d2,d3,d4,d5,d6,d7,d8AT=0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0the position of the restraintKAPPA=600.0,600.0,600.0,600.0,600.0,600.0,600.0,600.0specifies that the restraint is harmonic and what the values of the force constants on each of the variables are

#PRINT ARG=d1,d2,d3,d4,d5,d6,d7,d8 STRIDE=1000 FILE=slab-distances.dat

# Fill the reservoir with ions #dsres: DISTANCES GROUPA=p0 GROUPB=ncsoln MIN={BETA=50.} #rsres: RESTRAINT ARG=dsres.min AT=11.0 KAPPA=90000.0

#PRINT ARG=slabrest.bias,dsres.min,rsres.bias,rsres.force2 STRIDE=100 FILE=slab-res.dat

# CmuMDnsod:CMUMDGROUP=This action is not part of PLUMED and was included by using a LOAD command More detailsnasolnNSV=1 FIXED=0.51 DCR=0.217 CRSIZE=0.129 WF=0.0001 NINT=0.1 NZ=341nchl:CMUMDGROUP=This action is not part of PLUMED and was included by using a LOAD command More detailsclsolnNSV=1 FIXED=0.51 DCR=0.217 CRSIZE=0.129 WF=0.0001 NINT=0.1 NZ=341nwat:CMUMDGROUP=This action is not part of PLUMED and was included by using a LOAD command More detailswatoxyNSV=1 FIXED=0.51 DCR=0.217 CRSIZE=0.129 WF=0.0001 NINT=0.1 NZ=341RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=nsodthe arguments on which the bias is actingAT=1.8066the position of the restraintKAPPA=20000.0specifies that the restraint is harmonic and what the values of the force constants on each of the variables areLABEL=a label for the action so that its output can be referenced in the input to other actionsresnaRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=nchlthe arguments on which the bias is actingAT=1.8066the position of the restraintKAPPA=20000.0specifies that the restraint is harmonic and what the values of the force constants on each of the variables areLABEL=a label for the action so that its output can be referenced in the input to other actionsresclPrint quantities to a file. More detailsARG=nsod,nchl,nwat,the input for this action is the scalar output from one or more other actionsresna.bias,rescl.biasSTRIDE=50the frequency with which the quantities of interest should be outputFILE=COLVAR ... PRINTthe name of the file on which to output these quantities