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CSG_MAP(1)		    General Commands Manual		    CSG_MAP(1)

NAME
       csg_map - Part of the VOTCA package

SYNOPSIS
       csg_map [OPTIONS]

       csg_map [--help]

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).
	 * 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

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>

COPYRIGHT
       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)

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