Reference¶
Programs¶
csg_dlptopol¶
NAME¶
csg_dlptopol - Part of the VOTCA package
SYNOPSIS¶
csg_dlptopol [OPTIONS]
csg_dlptopol [–help]
DESCRIPTION¶
Create a dlpoly topology template based on an existing (atomistic) topology and a mapping xml-file. The created template file needs to be inspected and amended by the user!
EXAMPLES¶
* csg_dlptopol --top .dlpf --out .dlpf --cg cg-map.xml
convert FIELD to FIELD_CGV using cg-map.xml
* csg_dlptopol --top FA-dlpoly.dlpf --out CG-dlpoly.dlpf --cg cg-map.xml
* csg_dlptopol --top FA-gromacs.tpr --out FA-dlpoly.dlpf --no-map
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--out arg output topology in dlpoly format
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
csg_dump¶
NAME¶
csg_dump - Part of the VOTCA package
SYNOPSIS¶
csg_dump [OPTIONS]
csg_dump [–help]
DESCRIPTION¶
Print atoms that are read from topology file to help debugging atom naming.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;
Specific options:
--excl display exclusion list instead of molecule list
csg_fmatch¶
NAME¶
csg_fmatch - Part of the VOTCA package
SYNOPSIS¶
csg_fmatch [OPTIONS]
csg_fmatch [–help]
DESCRIPTION¶
Perform force matching (also called multiscale coarse-graining)
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--options arg options file for coarse graining
--trj-force arg coarse-grained trajectory containing forces of
already known interactions
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_gmxtopol¶
NAME¶
csg_gmxtopol - Part of the VOTCA package
SYNOPSIS¶
csg_gmxtopol [OPTIONS]
csg_gmxtopol [–help]
DESCRIPTION¶
Create skeleton for gromacs topology based on atomistic topology and a mapping file. File still needs to be modified by the user.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--out arg output topology (will create .top and in future also
.itp)
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
csg_imc_solve¶
NAME¶
csg_imc_solve - Part of the VOTCA package
SYNOPSIS¶
csg_imc_solve [OPTIONS]
csg_imc_solve [–help]
DESCRIPTION¶
Solves the linear system for IMCs
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
-r [ --regularization ] arg (=0) regularization factor
-i [ --imcfile ] arg imc statefile
-g [ --gmcfile ] arg gmc statefile
-n [ --idxfile ] arg idx statefile
csg_map¶
NAME¶
csg_map - Part of the VOTCA package
SYNOPSIS¶
csg_map [OPTIONS]
csg_map [–help]
DESCRIPTION¶
Convert a reference atomistic trajectory or configuration into a coarse-grained one based on a mapping xml-file. The mapping can be applied to either an entire trajectory or a selected set of frames only (see options).
EXAMPLES¶
* csg_map --top FA-topol.tpr --trj FA-traj.trr --out CG-traj.xtc --cg cg-map.xml
* csg_map --top FA-topol.tpr --trj FA-conf.gro --out CG-conf.gro --cg cg-map.xml
* csg_map --top FA-topol.tpr --trj FA-traj.xtc --out FA-history.dlph --no-map
* csg_map --top FA-field.dlpf --trj FA-history.dlph --out CG-history.dlph --cg cg-map.xml
* csg_map --top .dlpf --trj .dlph --out .dlph --cg cg-map.xml convert HISTORY to HISTORY_CGV
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--out arg output file for coarse-grained trajectory
--vel Write mapped velocities (if available)
--force Write mapped forces (if available)
--hybrid Create hybrid trajectory containing both atomistic
and coarse-grained
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_reupdate¶
NAME¶
csg_reupdate - Part of the VOTCA package
SYNOPSIS¶
csg_reupdate [OPTIONS]
csg_reupdate [–help]
DESCRIPTION¶
computes relative entropy update.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file (only needed for
RE update)
RE Specific options:
--options arg options file for coarse graining
--gentable arg (=0) only generate potential tables from given
parameters, NO RE update!
--interaction arg [OPTIONAL] generate potential tables only
for the specified interactions,
only valid when 'gentable' is true
--param-in-ext arg (=param.cur) Extension of the input parameter tables
--param-out-ext arg (=param.new) Extension of the output parameter tables
--pot-out-ext arg (=pot.new) Extension of the output potential tables
--hessian-check arg (=1) Disable the hessian check (mostly for
testing)
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works
for Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_stat¶
NAME¶
csg_stat - Part of the VOTCA package
SYNOPSIS¶
csg_stat [OPTIONS]
csg_stat [–help]
DESCRIPTION¶
Calculate all distributions (bonded and non-bonded) specified in options file. Optionally calculates update Eigen::Matrix3d for invere Monte Carlo. This program is called inside the inverse scripts. Big systems can be treated as well as non-bonded interactions can be evaluated.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;
Specific options:
--options arg options file for coarse graining
--do-imc write out additional Inverse Monte Carlo data
--include-intra do not exclude intramolecular neighbors
--block-length arg write blocks of this length, the averages are
cleared after every write
--ext arg (=dist.new) Extension of the output
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
Mapping file¶
The root node always has to be cg_molecule. It can contain the following keywords:
The following table contains the input options for CSG,
Property Name |
Default Value |
Description |
|---|---|---|
ident |
Molecule name in reference topology. |
|
topology |
Section defining coarse grained beads of molecule. |
|
topology.cg_beads |
Section defining coarse grained beads of molecule. |
|
topology.cg_beads.cg_bead |
Definition of a coarse grained bead. |
|
topology.cg_beads.cg_bead.name |
Name of coarse grained bead. |
|
topology.cg_beads.cg_bead.type |
Type of coarse grained bead. |
|
topology.cg_beads.cg_bead.mapping |
Mapping scheme to be used for this bead (specified in
section mapping) to map from reference system.
|
|
topology.cg_beads.cg_bead.beads |
The beads section lists all atoms of the reference system
that are mapped to this particular coarse grained bead.
The syntax is RESID:RESNAME:ATOMNAME, the beads are separated
by spaces.
|
|
topology.cg_bonded |
The cg_bonded section contains all bonded interaction
of the molecule. Those can be bond, angle or dihedral.
An entry for each group of bonded interaction can be specified,
e.g. several groups (types) of bonds can be specified.
A specific bonded interaction can be later on addressed
by MOLECULE:NAME:NUMBER, where MOLECULE is the molecule
ID in the whole topology, NAME the name of the interaction
group and NUMBER addresses the interaction in the group.
|
|
topology.cg_bonded.bond |
Definition of a group of bonds. |
|
topology.cg_bonded.bond.name |
Name of the bond. |
|
topology.cg_bonded.bond.beads |
List of pair of beads that define a bond. Names specified
in cg_beads
|
|
topology.cg_bonded.angle |
Definition of a group of angles. |
|
topology.cg_bonded.angle.name |
Name of the angle |
|
topology.cg_bonded.angle.beads |
List of triples of beads that define a bond. Names specified
in cg_beads
|
|
topology.cg_bonded.dihedral |
Definition of a group of dihedrals. Since the exact functional
form does not matter, this combines proper as well as
improper dihedrals.
|
|
topology.cg_bonded.dihedral.name |
Name of the dihedral |
|
topology.cg_bonded.dihedral.beads |
List of quadruples of beads that define a bond. Names
specified in cg_beads
|
|
maps |
Section containing definitions of mapping schemes. |
|
maps.map |
Section for a mapping for 1 bead. |
|
maps.map.name |
Name of the mapping |
|
maps.map.weights |
Weights of the mapping matrix. Entries are normalized
to 1, number of entries must match the number of reference
beads in a coarse-grained bead.
|
Topology file¶
The XMLtopology file
The XML topology root element, the base for the topology can be defined by the “name” attribute The following table contains the input options for CSG,
Property Name |
Default Value |
Description |
|---|---|---|
h5md_particle_group |
Attribute name holds the name of particles group in H5MD
file
|
|
molecules |
The the molecules in the trajectory or other operation
on the molecules.
|
|
molecules.molecule |
Definition of the molecule, with attributes: name, nmols
and nbeads. The name defines residue name, nmols tells
how many times this molecule has to be replicated to match
with trajectory file and nbeads defines number of beads
in every molecule.
|
|
molecules.molecule.bead |
Define the bead in the molecule. Attributes are: name
- the name of bead, type - the type of bead, mass - the
mass of bead, q - the value of charge and resid - the
id of the residue the bead belongs to (>=1).
|
|
molecules.clear |
Clear the information about the molecules |
|
molecules.rename |
Rename the molecules; attributes: “name” - the new name,
“range” - the range where the new name will be set in
the format start_range:end_range
|
|
molecules.define |
Define the molecules; attributes: “name” - the name of
molecule, “first” - the id of first molecule, “nbeads”
- the number of beads in the molecule, “nmols” - the number
of molecules
|
|
bonded |
This section defines the topology of the molecules, it
is used to generate proper exclusions for calculating
rdfs
|
|
bonded.bond |
Describes the bond |
|
bonded.bond.name |
The name of the bond |
|
bonded.bond.beads |
The pair of the beads in the format MOLECULE_NAME:BEAD_NAME
|
|
bonded.angle |
Describes the angle |
|
bonded.angle.name |
The name of the angle |
|
bonded.angle.beads |
The triplet of the beads in the format MOLECULE_NAME:BEAD_NAME
|
|
bonded.dihedral |
Describes the dihedrals |
|
bonded.dihedral.name |
The name of the dihedral |
|
bonded.dihedral.beads |
The quadruplet of the beads in the format MOLECULE_NAME:BEAD_NAME
|
|
beadtypes |
Allows defining bead types |
|
beadtypes.rename |
Rename the bead type; attributes: “name” - the old name,
“newname” - the new name
|
|
beadtypes.mass |
Define the mass of the bead type; attributes: “name” -
the bead type name, “value” - the new mass
|
csgapps¶
Extra user-contibuted applications based on the csg application class, that aren’t needed for the normal workflows. Installable with -DINSTALL_CSGAPPS=ON.
csg_fluctuations¶
NAME¶
csg_fluctuations - Part of the VOTCA package
SYNOPSIS¶
csg_fluctuations [OPTIONS]
csg_fluctuations [–help]
DESCRIPTION¶
calculate density fluctuations in subvolumes of the simulation box.Subolumes can be either cubic slabs in dimensions (x|y|z) or sphericalslabs with respect to either the center of box or a reference molecule
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Fluctuation options:
--filter arg (=*) filter molecule names
--rmax arg maximal distance to be considered
--rmin arg (=0) minimal distance to be considered
--refmol arg Reference molecule
--nbin arg (=100) Number of bins
--geometry arg (sphere|x|y|z) Take radial or x, y, z
slabs from rmin to rmax
--outfile arg (=fluctuations.dat) Output file
Mapping options:
--cg arg coarse graining mapping and bond
definitions (xml-file)
--map-ignore arg list of molecules to ignore separated by
;
--no-map disable mapping and act on original
trajectory
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works
for Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_orientcorr¶
NAME¶
csg_orientcorr - Part of the VOTCA package
SYNOPSIS¶
csg_orientcorr [OPTIONS]
csg_orientcorr [–help]
DESCRIPTION¶
Calculates the orientational correlation function <3/2*u(0)*u(r) - 1/2> for a polymer melt, where u is the vector pointing along a bond and r the distance between bond segments (centered on middle of bond).
The output is correlation.dat (with intra-molecular contributions) and correlation_excl.dat, where inter-molecular contributions are excluded.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Neighbor search options:
-c [ --cutoff ] arg (=1) cutoff for the neighbor search
--nbins arg (=40) number of bins for the grid
--nbmethod arg (=grid) neighbor search algorithm (simple or grid)
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_part_dist¶
NAME¶
csg_part_dist - Part of the VOTCA package
SYNOPSIS¶
csg_part_dist [OPTIONS]
csg_part_dist [–help]
DESCRIPTION¶
This program reads a topology and (set of) trajectory(ies). For every binned value of a chosen coordinate, it outputs the time-averaged number of particles, listed by particle types.
OPTIONS¶
Allowed options:
--top arg topology file
--trj arg trajectory file
--grid arg output grid spacing (min:step:max)
--out arg output particle distribution table
--ptypes arg particle types to include in the analysis
arg: file - particle types separated by space
default: all particle types
--first_frame arg first frame considered for analysis
--last_frame arg last frame considered for analysis
--coord arg coordinate analyzed ('x', 'y', or 'z' (default))
--shift_com shift center of mass to zero
--comment arg store a comment in the output table
--help produce this help message
csg_partial_rdf¶
NAME¶
csg_partial_rdf - Part of the VOTCA package
SYNOPSIS¶
csg_partial_rdf [OPTIONS]
csg_partial_rdf [–help]
DESCRIPTION¶
Calculate spatially confined rdfs
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;
Specific options:
--options arg options file defining the rdfs
--subvolume_radius arg Rdf calc. in spherical subvolume of this radius (from
center of box)
--do-vol-corr Correct for subvolume truncation in rdf
--write-every arg (UNIMPLEMENTED) write after every block of this
length, if --blocking is set, the averages are
cleared after every output
--do-blocks write output for blocking analysis
Threading options:
--nt arg (=1) number of threads
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_radii¶
NAME¶
csg_radii - Part of the VOTCA package
SYNOPSIS¶
csg_radii [OPTIONS]
csg_radii [–help]
DESCRIPTION¶
calculate gyration- and hydrodynamic radius for a specific molecule or molecule type
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Molecule filter options:
--mol arg molecule number
--molname arg (=*) pattern for molecule name
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_sphericalorder¶
NAME¶
csg_sphericalorder - Part of the VOTCA package
SYNOPSIS¶
csg_sphericalorder [OPTIONS]
csg_sphericalorder [–help]
DESCRIPTION¶
- !! EXPERIMENTAL !! Calculate spherical order parameter.
Needs non-spherical beads in mapping.
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--filter arg (=*) filter molecule names
--radialcut arg (=0) radial cutoff: distance from center where bead is
considered
--minrad arg (=0) minimal distance a parcle has to be apart from center
to be considerd
--refmol arg Reference molecule
--rbinw arg (=0) Do multiple r_bins multiple histograms
Mapping options:
--cg arg coarse graining mapping and bond definitions
(xml-file)
--map-ignore arg list of molecules to ignore separated by ;
--no-map disable mapping and act on original trajectory
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_traj_force¶
NAME¶
csg_traj_force - Part of the VOTCA package
SYNOPSIS¶
csg_traj_force [OPTIONS]
csg_traj_force [–help]
DESCRIPTION¶
Adds/subtracts forces from given atomistic trajectories
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
--scale arg (=-1) scaling factor for trajectory forces
--trj-force arg atomistic reference trajectory containing forces to
add/subtract
--out arg output trajectory file with resultant forces
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames
csg_density¶
NAME¶
csg_density - Part of the VOTCA package
SYNOPSIS¶
csg_density [OPTIONS]
csg_density [–help]
DESCRIPTION¶
Calculates the mass density distribution along a box axis or radial density profile from reference point
OPTIONS¶
Allowed options:
-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file
Mapping options:
--cg arg [OPTIONAL] coarse graining mapping and bond
definitions
(xml-file). If no file is given, program acts on
original trajectory
--map-ignore arg list of molecules to ignore if mapping is done
separated by ;
Specific options::
--type arg (=mass) density type: mass or number
--axis arg (=r) [x|y|z|r] density axis (r=spherical)
--step arg (=0.01) spacing of density
--block-length arg write blocks of this length, the averages are
cleared after every write
--out arg Output file
--rmax arg rmax (default for [r] =min of all box vectors/2, else
l )
--scale arg (=1) scale factor for the density
--molname arg (=*) molname
--filter arg (=*) filter bead names
--ref arg reference zero point
Trajectory options:
--trj arg atomistic trajectory file
--begin arg (=0) skip frames before this time (only works for
Gromacs files)
--first-frame arg (=0) start with this frame
--nframes arg process the given number of frames