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csg_map - Man Page

Part of the VOTCA package


csg_map [Options]

csg_map [--help]


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).
 * 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


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
   --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


Written and maintained by the VOTCA Development Team <devs@votca.org>


csg_map User Manual VOTCA Development Team