Documentation‎ > ‎Coarse-graining‎ > ‎

programs

csg_boltzmann

Performs tasks that are needed for simple boltzmann inversion in an interactive environment.

Allowed options:

  • -h [ --help ] display this help and exit
  • -v [ --verbose ] be loud and noisy
  • --top arg atomistic topology 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 Special options:
  • --excl arg write exclusion list to file

Trajectory options:

  • --trj arg atomistic trajectory file
  • --begin arg (=0) skip frames before this time
  • --first-frame arg (=0) start with this frame
  • --nframes arg process the given number of frames

csg_call

This script calls scripts and functions for the iterative framework. Function can be executed or shows if key1='function'.

Usage: csg_call [OPTIONS] key1 key2 [SCRIPT OPTIONS]

Allowed options:

  • -l, --list Show list of all script
  • --cat Show the content of the script
  • --show Show the path to the script
  • --show-share Shows the used VOTCASHARE dir and exits
  • --scriptdir DIR Set the user script dir (Used if no options xml file is given) Default: empty
  • --simprog PROG Set the simprog (Used if no options xml file is given) Default: empty
  • --options FILE Specify the options xml file to use
  • --log FILE Specify the log file to use Default: stdout
  • --ia-type type Specify the interaction type to use
  • --ia-name name Specify the interaction name to use
  • --nocolor Disable colors
  • --sloppy-tables Allow tables without flags
  • --debug Enable debug mode with a lot of information
  • -h, --help Show this help

Examples:

  • csg_call table smooth [ARGUMENTS]
  • csg_call --show run gromacs

csg_density

Calculates the mass density distribution along a box axis or radial density profile from reference point

Allowed options:

  • -h [ --help ] display this help and exit
  • -v [ --verbose ] be 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::

  • --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
  • --first-frame arg (=0) start with this frame
  • --nframes arg process the given number of frames

csg_dump

Print atoms that are read from topology file to help debugging atom naming.

Allowed options:

  • -h [ --help ] display this help and exit
  • -v [ --verbose ] be 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

Perform force matching (also called multiscale coarse-graining)

Allowed options:

  • -h [ --help ] display this help and exit
  • -v [ --verbose ] be 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
  • --first-frame arg (=0) start with this frame
  • --nframes arg process the given number of frames

csg_gmxtopol

Create skeleton for gromacs topology based on atomistic topology and a mapping file. File still needs to be modified by the user.

Allowed options:

  • -h [ --help ] display this help and exit
  • -v [ --verbose ] be 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_imcrepack

This program is internally called by inversion scripts to kick out zero entries in matrix for inverse Monte Carlo. It also extracts the single potential updates out of the full solution.

Allowed options:

  • --in arg files to read
  • --out arg files to write
  • --unpack arg extract all tables from this file
  • --help display help message

csg_inverse

Start the script to run ibi, imc, etc. or clean out current dir

Usage: csg_inverse [OPTIONS] --options settings.xml [clean]

Allowed options:

  • -h, --help show this help
  • -N, --do-iterations N only do N iterations
  • --wall-time SEK Set wall clock time
  • --options FILE Specify the options xml file to use
  • --debug enable debug mode with a lot of information
  • --nocolor disable colors

Examples:

  • csg_inverse --options cg.xml
  • csg_inverse -6 --options cg.xml

csg_map

Map a reference trajectory to a coarse-grained trajectory. This program can be used to map a whole trajectory or to create an initial configuration for a coarse-grained run only.

Allowed options:

  • -h [ --help ] display this help and exit
  • -v [ --verbose ] be loud and noisy
  • --top arg atomistic topology file
  • --out arg output file for coarse-grained trajectory
  • --vel Write mapped velocities (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
  • --first-frame arg (=0) start with this frame
  • --nframes arg process the given number of frames

csg_property

Helper program called by inverse scripts to parse xml file.

Allowed options:

  • --help produce this help message
  • --path arg list option values that match given criteria
  • --filter arg list option values that match given criteria
  • --print arg (=.) list option values that match given criteria
  • --file arg xml file to parse
  • --short short version of output
  • --with-path include path of node in output

csg_resample

Change grid and interval of any sort of table files. Mainly called internally by inverse script, can also be used to manually prepare input files for coarse-grained simulations.

Allowed options:

  • --help produce this help message
  • --in arg table to read
  • --out arg table to write
  • --derivative arg table to write
  • --grid arg new grid spacing (min:step:max). If 'grid' is specified only, interpolation is performed.
  • --type arg (=akima) [cubic|akima|linear]. If option is not specified, the default type 'akima' is assumed.
  • --fitgrid arg specify fit grid (min:step:max). If 'grid' and 'fitgrid' are specified, a fit is performed.
  • --nocut Option for fitgrid: Normally, values out of fitgrid boundaries are cut off. If they shouldn't, choose --nocut.
  • --comment arg store a comment in the output table
  • --boundaries arg (natural|periodic|derivativezero) sets boundary conditions

csg_stat

Calculate all distributions (bonded and non-bonded) specified in options file. Optionally calculates update matrix for invere Monte Carlo. This program is called inside the inverse scripts. Unlike csg_boltzmann, big systems can be treated as well as non-bonded interactions can be evaluated.

Allowed options:

  • -h [ --help ] display this help and exit
  • -v [ --verbose ] be 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
  • --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
  • --first-frame arg (=0) start with this frame
  • --nframes arg process the given number of frames

multi_g_rdf

This is a multiplexed version of g_rdf

Usage: multi_g_rdf [OPTIONS] -- [g_rdf_options]

Allowed options:

  • -N, --NN Number of tasks Default: 8
  • -b TIME Begin time Default: 0
  • -e TIME End time
  • -n FILE Name of the index file Default: index.ndx
  • -o FILE.xvg Name of the total output file Default: rdf.xvg
  • --soutput FILE.xvg Name of the single output files Default: rdf_NP.xvg (used trunc of name given by -o) (where NP is replaced later by the number of the process)
  • --log FILE Name of logfile Default: rdf_NP.log" (used trunc of name given by -o) (where NP is replaced later by the number of the process)
  • --cmd CMD Change the gromacs command to run Default: g_rdf
  • --single Run only one task at the time
  • --debug Enable debug output
  • -q, --quiet Be a little bit quiet
  • -h, --help Show this help

Examples:

  • multi_g_rdf -e 1
  • multi_g_rdf -e 1 -- -bin 0.05
Comments