Project ID: plumID:23.041
Source: 05-7b5o/2-Production/cc-1.0/plumed_EMMI.dat
Originally used with PLUMED version: 2.10
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
# if you are restarting the run, please uncomment this line
#RESTART
# include topology info

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
=../../1-Data/step3_input_xtc.pdb 
WHOLE
 The reference structure is whole, i

# define map atoms
system-map: 
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)
=../../1-Data/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=System-MAP
# define protein atoms
system-pro: 
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)
=../../1-Data/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=System-PRO
# make protein whole

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
=system-pro 
STRIDE
 the frequency with which molecules are reassembled
=4
# Wrap water around protein
wrap-at: 
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)
=index-wrap.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Wrap-ATOMS
wrap-ar: 
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)
=index-wrap.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Wrap-AROUND

WRAPAROUND
Rebuild periodic boundary conditions around chosen atoms. More details
 
ATOMS
wrapped atoms
=wrap-at 
AROUND
reference atoms
=wrap-ar 
PAIR
 Pair atoms in AROUND and ATOMS groups
 
STRIDE
 the frequency with which molecules are reassembled
=4

# 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
=emmi
# general parameters - do not change this!
# NL_STRIDE: update neighbor list stride
# NL_DIST_CUTOFF: distance cutoff in nm
# NL_GAUSS_CUTOFF: cutoff based on the Gaussian sigma

TEMP
temperature
=300.0 
NL_STRIDE
neighbor list update frequency
=50 
NL_DIST_CUTOFF
neighbor list distance cutoff
=1.0 
NL_GAUSS_CUTOFF
neighbor list Gaussian sigma cutoff
=3.0
# define atoms for cryo-EM restraint and read experimental data

ATOMS
atoms used in the calculation of the density map, typically all heavy atoms
=system-map 
DATA_FILE
file with cryo-EM map
=emd_plumed_aligned.dat
# info about the experimental map

NORM_DENSITY
integral of experimental density
=2660.966064 
RESOLUTION
cryo-EM map resolution
=0.25
# data likelihood (or noise model): Marginal

SIGMA_MIN
minimum density error
=0.2 
GPU
 calculate EMMIVOX on GPU with Libtorch

# output: in production write with the frequency at which XTC/TRR are written

STATUS_FILE
write a file with all the data useful for restart
=EMMIStatus 
WRITE_STRIDE
stride for writing status file
=5000
# comment this if you have a hetero-complex
#BFACT_NOCHAIN
# in production, you should sample Bfactors

DBFACT
Bfactor MC step
=0.05 
MCBFACT_STRIDE
Bfactor MC stride
=500 
BFACT_SIGMA
Bfactor sigma prior
=0.1
# scale factor

SCALE
scale factor
=1.450000
# correlation

CORRELATION
 calculate correlation coefficient

...

# in production, apply bias to system
# translate into bias - updated every 2/4 time steps
# emr: BIASVALUE ARG=emmi.scoreb STRIDE=2
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
=emmi.scoreb 
STRIDE
the frequency with which the forces due to the bias should be calculated
=4
#
# include water positional restraint

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=../../1-Data/plumed_posres.dat
#
# 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
=emmi 
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
=5000