1csg_map(1)                  General Commands Manual                 csg_map(1)
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NAME

6       csg_map - Part of the VOTCA package
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SYNOPSIS

10       csg_map [OPTION] [OPTIONPARAMETERS]
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DESCRIPTION

14       Convert  a  reference  atomistic  trajectory  or  configuration  into a
15       coarse-grained one based on a mapping  xml-file.  The  mapping  can  be
16       applied to either an entire trajectory or a selected set of frames only
17       (see  options).   Examples:  *   csg_map   --top   FA-topol.tpr   --trj
18       FA-traj.trr   --out   CG-traj.xtc   --cg  cg-map.xml  *  csg_map  --top
19       FA-topol.tpr --trj FA-conf.gro  --out  CG-conf.gro  --cg  cg-map.xml  *
20       csg_map  --top  FA-topol.tpr  --trj  FA-traj.xtc  --out FA-history.dlph
21       --no-map * csg_map  --top  FA-field.dlpf  --trj  FA-history.dlph  --out
22       CG-history.dlph --cg cg-map.xml * csg_map --top .dlpf --trj .dlph --out
23       .dlph --cg cg-map.xml  convert HISTORY to HISTORY_CGV
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26       Please visit the program site at __http://www.votca.org__.
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OPTIONS

30       Allowed options:
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33       -h [ --help ]
34              display this help and exit
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36       -v [ --verbose ]
37              be loud and noisy
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39       --top arg
40              atomistic topology file
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42       --out arg
43              output file for coarse-grained trajectory
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45       --vel  Write mapped velocities (if available)
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47       --force
48              Write mapped forces (if available)
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50       --hybrid
51              Create  hybrid  trajectory   containing   both   atomistic   and
52              coarse-grained
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55       Mapping options:
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58       --cg arg
59              coarse graining mapping and bond definitions (xml-file)
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61       --map-ignore arg
62              list of molecules to ignore separated by ;
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64       --no-map
65              disable mapping and act on original trajectory
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68       Trajectory options:
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71       --trj arg
72              atomistic trajectory file
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74       --begin arg (=0)
75              skip frames before this time (only works for Gromacs files)
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77       --first-frame arg (=0)
78              start with this frame
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80       --nframes arg
81              process the given number of frames
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AUTHORS

85       Written and maintained by the VOTCA Development Team <devs@votca.org>
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88       This  Manual  Page  was converted from t2t format to the this format by
89       txt2tags (http://txt2tags.org) !   The  t2t  file  was  extracted  from
90       'csg_map --help' by help2t2t (version 1.5.1 )
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94       Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
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97       Licensed under the Apache License, Version 2.0 (the "License"); you may
98       not use this file except in  compliance  with  the  License.   You  may
99       obtain a copy of the License at
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102           http://www.apache.org/licenses/LICENSE-2.0
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105       Unless  required  by  applicable  law or agreed to in writing, software
106       distributed under the License is distributed on an "AS IS" BASIS, WITH‐
107       OUT  WARRANTIES  OR  CONDITIONS OF ANY KIND, either express or implied.
108       See the License for the specific  language  governing  permissions  and
109       limitations under the License.
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116Version: 1.5.1                2019-11-22 00:00:00                   csg_map(1)
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