.TH "CSG_MAP" "1" " csg_map User Manual" "VOTCA Development Team"
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.SH NAME
.PP
\fBcsg_map\fP \- Part of the VOTCA package


.SH SYNOPSIS
.PP
\fBcsg_map\fP [OPTIONS]
.PP
\fBcsg_map\fP [\-\-help]


.SH DESCRIPTION
.PP

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
  
  
  

.SH OPTIONS
.PP

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

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


.SH COPYRIGHT
.PP

Copyright 2009\-2021 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.