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