PLUMED-NEST

Project ID: plumID:20.015
Source: 2-EMMI/plumed.dat
Originally used with PLUMED version: 2.6-dev
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

# uncomment next line if your restart
#RESTART

# load extra file
# set to correct location
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
The LOAD action with label  calculates something
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
=../0-TOPO/step5_charmm2gmx.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)
=../0-TOPO/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=PROT-H

# make protein whole and in the cell where map is defined
The GROUP action with label protein-h calculates something
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
=1-6701
ENTITY1
the atoms that make up a molecule that you wish to align
=6702-6741
... WHOLEMOLECULES

# create EMMI score
EMMIVOX
Bayesian single-structure and ensemble refinement with cryo-EM maps. More details
 ...
# name of this action
LABEL
a label for the action so that its output can be referenced in the input to other actions
=gmm
# general parameters - do not change this! 
TEMP
temperature
=303.15 
NL_STRIDE
neighbor list update frequency
=50 NL_CUTOFF=0.5 NS_CUTOFF=1.0
# define atoms for cryo-EM restraint and read experimental data
# set path to map file if not in current directory
ATOMS
atoms used in the calculation of the density map, typically all heavy atoms
=protein-h 
DATA_FILE
file with cryo-EM map
=map_zoned_align.dat
# info about the experimental map
NORM_DENSITY
integral of experimental density
=2068.185 
RESOLUTION
cryo-EM map resolution
=0.1 VOXEL=0.1012
# data likelihood (or noise model): Marginal
NOISETYPE=MARGINAL 
SIGMA_MIN
minimum density error
=0.2
# write output
STATUS_FILE
write a file with all the data useful for restart
=EMMIStatus 
WRITE_STRIDE
stride for writing status file
=2500
...

# translate into bias - updated every 2 time steps
The EMMIVOX action with label gmm calculates the following quantities:
 Quantity   
 Description  
gmm.scoreb
Bayesian score
gmm.scale
scale factor
gmm.offset
offset
gmm.accB
Bfactor MC acceptance
gmm.kbt
temperature in energy unitemr: 
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
The BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Description  
emr.bias
the instantaneous value of the bias potential
emr._bias
one or multiple instances of this quantity can be referenced elsewhere in the input 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