Project ID: plumID:19.007
Source: EMMI-MT/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
tested onv2.9
tested onmaster
# include topology info: this is needed to identify atom types

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
=structure.pdb 
WHOLE
 The reference structure is whole, i

# define all heavy atoms using GROMACS index file
# which can be created with gmx_mpi make_ndx
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)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H
protein: 
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.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein
protein-no-negative: 
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.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-no-negative-no-h
# make protein whole: add reference position of first heavy atom (in nm)

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
=protein
# create EMMI score

EMMI
Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details
 ...

LABEL
a label for the action so that its output can be referenced in the input to other actions
=gmm 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
TEMP
temperature
=300.0 
NL_STRIDE
The frequency with which we are updating the neighbor list
=50 
NL_CUTOFF
The cutoff in overlap for the neighbor list
=0.01

ATOMS
atoms for which we calculate the density map, typically all heavy atoms
=protein-no-negative 
GMM_FILE
file with the parameters of the GMM components
=AC_SYMM.dat
#ATOMS selects what is refined
# no-negative-no-h or no-h are reasonable
# resolution is not used - no Bfactor fitting
# SIGMA_MIN can go down to 0.02, must be > NL_CUTOFF,
# if crashes, raise back to 0.05,
# the larger the number the softer the contribution of the EM data

SIGMA_MIN
minimum uncertainty
=0.05 
RESOLUTION
Cryo-EM map resolution
=0.1 
NOISETYPE
functional form of the noise (GAUSS, OUTLIERS, MARGINAL)
=MARGINAL
...

# translate into bias
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 useful info 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
=500