1CSG_MAP(1)                  General Commands Manual                 CSG_MAP(1)
2
3
4

NAME

6       csg_map - Part of the VOTCA package
7
8
9

SYNOPSIS

11       csg_map [OPTIONS]
12
13       csg_map [--help]
14
15
16

DESCRIPTION

18       Convert a reference atomistic trajectory or configuration into a
19       coarse-grained one based on a mapping xml-file. The mapping can be
20       applied to either an entire trajectory or a selected set of frames only
21       (see options).
22         * csg_map --top FA-topol.tpr --trj FA-traj.trr --out CG-traj.xtc --cg
23       cg-map.xml
24         * csg_map --top FA-topol.tpr --trj FA-conf.gro --out CG-conf.gro --cg
25       cg-map.xml
26         * csg_map --top FA-topol.tpr --trj FA-traj.xtc --out FA-history.dlph
27       --no-map
28         * csg_map --top FA-field.dlpf --trj FA-history.dlph --out CG-
29       history.dlph --cg cg-map.xml
30         * csg_map --top .dlpf --trj .dlph --out .dlph --cg cg-map.xml
31       convert HISTORY to HISTORY_CGV
32
33
34
35
36

OPTIONS

38       Allowed options:
39
40           -h [ --help ]             display this help and exit
41           --verbose                 be loud and noisy
42           --verbose1                be very loud and noisy
43           -v [ --verbose2 ]         be extremly loud and noisy
44           --top arg                 atomistic topology file
45           --out arg                 output file for coarse-grained trajectory
46           --vel                     Write mapped velocities (if available)
47           --force                   Write mapped forces (if available)
48           --hybrid                  Create hybrid trajectory containing both
49       atomistic
50                                   and coarse-grained
51         Mapping options:
52
53           --cg arg                  coarse graining mapping and bond
54       definitions
55                                   (xml-file)
56           --map-ignore arg          list of molecules to ignore separated by
57       ;
58           --no-map                  disable mapping and act on original
59       trajectory
60         Trajectory options:
61
62           --trj arg                 atomistic trajectory file
63           --begin arg (=0)          skip frames before this time (only works
64       for
65                                   Gromacs files)
66           --first-frame arg (=0)    start with this frame
67           --nframes arg             process the given number of frames
68
69

AUTHORS

71       Written and maintained by the VOTCA Development Team <devs@votca.org>
72
73
74

76       Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
77
78       Licensed under the Apache License, Version 2.0 (the "License"); you may
79       not use this  file except in compliance with the License.  You may
80       obtain a copy of the License at
81
82              http://www.apache.org/licenses/LICENSE-2.0
83
84       Unless  required by applicable law or agreed to in writing, software
85       distributed under the License is distributed on an "AS IS" BASIS,
86       WITHOUT WARRANTIES OR CONDITIONS OF ANY  KIND, either  express  or
87       implied.   See  the  License  for  the  specific  language  governing
88       permissions and limitations under the License.
89
90
91
92
93VOTCA Development Team        csg_map User Manual                   CSG_MAP(1)
Impressum