csg_map - Part of the VOTCA package

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

       Copyright 2009-2024 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.

VOTCA Development Team                         csg_map User Manual                                    CSG_MAP(1)

       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

csg_map - Part of the VOTCA package

       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

csg_map [OPTIONS]

       csg_map [--help]