Project ID: plumID:22.018
Source: LAT1/plumed.dat
Originally used with PLUMED version: 2.7
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 onv2.8
tested onmaster
tested on master
####### Edited by KKH on 08/17/21  #############
# load extra file
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=EMMIVox.cpp
# include topology info - set path a PDB file
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
STRUCTURE
a file in pdb format containing a reference structure
=gromacs.pdb
WHOLE
The reference structure is whole, i

# define all heavy atoms - set path to index file protein-h:
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
NDX_FILE
the name of index file (gromacs syntax)
=index2.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H_lig-H
# make protein whole and in the cell where map is defined
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
...
ADDREFERENCE
Define the reference position of the first atom of each entity using a PDB file
EMST
Define atoms sequence in entities using an Euclidean minimum spanning tree
ENTITY0
the atoms that make up a molecule that you wish to align
=1-7317
ENTITY1
the atoms that make up a molecule that you wish to align
=7318-7368 ... WHOLEMOLECULES
# create EMMI score # parameters #NEED TO EDIT gmm:
EMMIVOX
This action is not part of PLUMED and was included by using a LOAD command More details
TEMP=300.0 NL_STRIDE=50 NL_CUTOFF=0.5 NS_CUTOFF=1.0 NO_AVER ATOMS=protein-h DATA_FILE=map_plumed_align.dat NORM_DENSITY=1354.3429 RESOLUTION=0.1 VOXEL=0.1087 SIGMA_MIN=0.2 STATUS_FILE=EMMIStatus WRITE_STRIDE=2500 NOISETYPE=MARGINAL
# translate into bias - updated every 2 time steps emr:
BIASVALUE
Takes the value of one variable and use it as a bias More details
ARG
the input for this action is the scalar output from one or more other actions
=gmm.scoreb
STRIDE
the frequency with which the forces due to the bias should be calculated
=2
# print output to file
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=gmm
FILE
the name of the file on which to output these quantities
=COLVAR
STRIDE
the frequency with which the quantities of interest should be output
=2500