PLUMED-NEST

Project ID: plumID:21.011
Source: NaCl_at_graphite-cmumd/cmumd.plmd
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 (v2) input file to implement CmuMD
# Please consider citing Perego et al. J Chem Phys 142, 144113 (2015)
# Please consider citing Finney et al. 

# CmuMD is not yet implemented in Plumed
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=Cmumd.cpp

# Define groups of atoms
The LOAD action with label  calculates somethinggra: 
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
=1-9152:1 
The GROUP action with label gra calculates somethingsod: 
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
=43320-43737:1
The GROUP action with label sod calculates somethingchl: 
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
=43738-44155:1
The GROUP action with label chl calculates somethingslt: 
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
=43320-44155:1
The GROUP action with label slt calculates somethingwat: 
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
=9153-43319:1
The GROUP action with label wat calculates somethingsln: 
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
=9153-44155:1 
The GROUP action with label sln calculates somethingall: 
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
=1-44155:1

# Provide parameters for the CV
The GROUP action with label all calculates somethingnwat: 
CMUMD
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUP=wat NSV=3 DCR=0.25 CRSIZE=0.15 WF=0.0001 NINT=1.0 NZ=291
nsod: 
CMUMD
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUP=sod NSV=1 FIXED=0.5 DCR=0.25 CRSIZE=0.15 WF=0.0001 NINT=0.1 NZ=291
nchl: 
CMUMD
This action is not part of PLUMED and was included by using a LOAD command More details
 GROUP=chl NSV=1 FIXED=0.5 DCR=0.25 CRSIZE=0.15 WF=0.0001 NINT=0.1 NZ=291

# CmuMD is implemented as a restraint on the densities of species in CR
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
=0.3011 
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
=0.3011 
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
#RESTRAINT ARG=n_water AT=29.5 KAPPA=20.0 LABEL=wres


# Report the densities and bias
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