csg_map - Man Page

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
                           (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

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.