PLUMED-NEST

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

Click on the labels of the actions for more information on what each action computes

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

# Define the groups
The LOAD action with label  calculates somethingnaslab: 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=1-1921
The GROUP action with label naslab calculates somethingclslab: 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=1922-3842
The GROUP action with label clslab calculates somethingncslab: 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=1-3842
The GROUP action with label ncslab calculates somethingwatoxy: 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=3843-45297:3
The GROUP action with label watoxy calculates somethingnasoln: 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=1-1921,45300-46971
The GROUP action with label nasoln calculates somethingclsoln: 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=1922-3842,46972-48643
The GROUP action with label clsoln calculates somethingncsoln: 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=1-3842,45300-48643


# Middle of the slab
#p0: FIXEDATOM AT=2.88992,2.88992,8.51019
The GROUP action with label ncsoln calculates somethingp0: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.88992,2.88992,8.65

# Restrain the slab
The FIXEDATOM action with label p0 calculates somethingp1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=1.965,2.154,8.214   # 535
The FIXEDATOM action with label p1 calculates somethingp2: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.692,2.153,8.212   # 547
The FIXEDATOM action with label p2 calculates somethingp3: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=1.969,3.892,8.211   # 655
The FIXEDATOM action with label p3 calculates somethingp4: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.687,3.880,8.227   # 667
The FIXEDATOM action with label p4 calculates somethingp5: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=1.959,2.147,8.794   # 935
The FIXEDATOM action with label p5 calculates somethingp6: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.699,2.147,8.811   # 947
The FIXEDATOM action with label p6 calculates somethingp7: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=1.963,3.889,8.796   #1055
The FIXEDATOM action with label p7 calculates somethingp8: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.710,3.904,8.806   #1067

The FIXEDATOM action with label p8 calculates somethingd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p1,535
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p2,547 
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p3,655 
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p4,667
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p5,935 
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p6,947 
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p7,1055 
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomsd8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p8,1067

The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomsslabrest: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=d1,d2,d3,d4,d5,d6,d7,d8 ATthe position of the restraint=0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=600.0,600.0,600.0,600.0,600.0,600.0,600.0,600.0

#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

# CmuMD
The RESTRAINT action with label slabrest calculates the following quantities:
 Quantity   
 Description  
slabrest.bias
the instantaneous value of the bias potential
slabrest.force2
the instantaneous value of the squared force due to this bias potentialnsod: CMUMDThis action is not part of PLUMED and was included by using a LOAD command More details GROUP=nasoln NSV=1 FIXED=0.51 DCR=0.217 CRSIZE=0.129 WF=0.0001 NINT=0.1 NZ=341
nchl: CMUMDThis action is not part of PLUMED and was included by using a LOAD command More details GROUP=clsoln NSV=1 FIXED=0.51 DCR=0.217 CRSIZE=0.129 WF=0.0001 NINT=0.1 NZ=341
nwat: CMUMDThis action is not part of PLUMED and was included by using a LOAD command More details GROUP=watoxy NSV=1 FIXED=0.51 DCR=0.217 CRSIZE=0.129 WF=0.0001 NINT=0.1 NZ=341

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=1.8066 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=1.8066 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

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