NAME

       csg_map - Part of the VOTCA package

SYNOPSIS

       csg_map [OPTION] [OPTIONPARAMETERS]

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

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

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

AUTHORS

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

       This  Manual  Page  was  converted from t2t format to the this format by txt2tags (http://txt2tags.org) !
       The t2t file was extracted from 'csg_map --help' by help2t2t (version 1.6_rc1 )

COPYRIGHT

       Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)

       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

           http://www.apache.org/licenses/LICENSE-2.0

       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.