Provided by: votca-csg_1.5-3_amd64 bug


       csg_map - Part of the VOTCA package




       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

       Please visit the program site at __http://www.votca.org__.


       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)

              Write mapped forces (if available)

              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 ;

              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 <>

       This  Manual  Page  was  converted  from  t2t  format  to  the  this  format  by  txt2tags
       (  !   The  t2t  file  was extracted from 'csg_map --help' by help2t2t
       (version 1.5 )


       Copyright 2009-2011 The VOTCA Development Team (

       Licensed under the Apache License, Version 2.0 (the "License"); you may not use this  file
       except in compliance with the License.  You may obtain a copy of the License at


       Unless  required by applicable law or agreed to in writing, software distributed under the
       License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY  KIND,
       either  express  or  implied.   See  the  License  for  the  specific  language  governing
       permissions and limitations under the License.