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
tested onv2.9
tested onmaster
tested on master
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=Cmumd.cpp
# Define the groups naslab:
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
=1-1921 clslab:
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
=1922-3842 ncslab:
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
=1-3842 watoxy:
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
=3843-45297:3 nasoln:
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
=1-1921,45300-46971 clsoln:
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
=1922-3842,46972-48643 ncsoln:
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
=1-3842,45300-48643
# Middle of the slab #p0: FIXEDATOM AT=2.88992,2.88992,8.51019 p0:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=2.88992,2.88992,8.65
# Restrain the slab p1:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=1.965,2.154,8.214 # 535 p2:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=3.692,2.153,8.212 # 547 p3:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=1.969,3.892,8.211 # 655 p4:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=3.687,3.880,8.227 # 667 p5:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=1.959,2.147,8.794 # 935 p6:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=3.699,2.147,8.811 # 947 p7:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=1.963,3.889,8.796 #1055 p8:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=3.710,3.904,8.806 #1067
d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=p1,535 d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=p2,547 d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=p3,655 d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=p4,667 d5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=p5,935 d6:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=p6,947 d7:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=p7,1055 d8:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=p8,1067
slabrest:
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
ARG
the arguments on which the bias is acting
=d1,d2,d3,d4,d5,d6,d7,d8
AT
the 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 nsod:
CMUMD
This 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:
CMUMD
This 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:
CMUMD
This 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
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
=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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=resna
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
=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
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rescl
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