PLUMED-NEST

Project ID: plumID:21.035
Source: CmuMD-NaCl/flat-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

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=Cmumd.cpp

# Define the groups
The LOAD action with label  calculates somethingnaslab: 
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
=1-2000
The GROUP action with label naslab calculates somethingclslab: 
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
=2001-4000
The GROUP action with label clslab calculates somethingncslab: 
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
=1-4000
The GROUP action with label ncslab calculates somethingwatoxy: 
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
=4001-45455:3
The GROUP action with label watoxy calculates somethingnasoln: 
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
=45458-47129
The GROUP action with label nasoln calculates somethingclsoln: 
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
=47130-48801
The GROUP action with label clsoln calculates somethingncsoln: 
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
=45458-48801

# Middle of the slab
#p0: FIXEDATOM AT=2.88992,2.88992,8.51019
The GROUP action with label ncsoln calculates somethingp0: 
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
The FIXEDATOM action with label p0 calculates somethingp1: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=1.965,2.154,8.214   # 535
The FIXEDATOM action with label p1 calculates somethingp2: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=3.692,2.153,8.212   # 547
The FIXEDATOM action with label p2 calculates somethingp3: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=1.969,3.892,8.211   # 655
The FIXEDATOM action with label p3 calculates somethingp4: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=3.687,3.880,8.227   # 667
The FIXEDATOM action with label p4 calculates somethingp5: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=1.959,2.147,8.794   # 935
The FIXEDATOM action with label p5 calculates somethingp6: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=3.699,2.147,8.811   # 947
The FIXEDATOM action with label p6 calculates somethingp7: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=1.963,3.889,8.796   #1055
The FIXEDATOM action with label p7 calculates somethingp8: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=3.710,3.904,8.806   #1067

The FIXEDATOM action with label p8 calculates somethingd1: 
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
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: 
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 
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: 
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 
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: 
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
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: 
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 
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: 
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 
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd7: 
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 
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomsd8: 
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

The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomsslabrest: 
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
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: 
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
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
=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

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