
NAME
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**csg_map** - Part of the VOTCA package

SYNOPSIS
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**csg_map** [OPTIONS]

**csg_map** [--help]



DESCRIPTION
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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
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::

    * 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
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  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
