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

NAME

6       csg_map - Part of the VOTCA package
7

SYNOPSIS

9       csg_map [OPTION] [OPTIONPARAMETERS]
10

DESCRIPTION

12       Convert  a  reference  atomistic  trajectory  or  configuration  into a
13       coarse-grained one based on a mapping  xml-file.  The  mapping  can  be
14       applied to either an entire trajectory or a selected set of frames only
15       (see  options).   Examples:  *   csg_map   --top   FA-topol.tpr   --trj
16       FA-traj.trr   --out   CG-traj.xtc   --cg  cg-map.xml  *  csg_map  --top
17       FA-topol.tpr --trj FA-conf.gro  --out  CG-conf.gro  --cg  cg-map.xml  *
18       csg_map  --top  FA-topol.tpr  --trj  FA-traj.xtc  --out FA-history.dlph
19       --no-map * csg_map  --top  FA-field.dlpf  --trj  FA-history.dlph  --out
20       CG-history.dlph --cg cg-map.xml * csg_map --top .dlpf --trj .dlph --out
21       .dlph --cg cg-map.xml  convert HISTORY to HISTORY_CGV
22
23       Please visit the program site at __http://www.votca.org__.
24

OPTIONS

26       Allowed options:
27
28
29       -h [ --help ]
30              display this help and exit
31
32       --verbose
33              be loud and noisy
34
35       --verbose1
36              be very loud and noisy
37
38       -v [ --verbose2 ]
39              be extremly loud and noisy
40
41       --top arg
42              atomistic topology file
43
44       --out arg
45              output file for coarse-grained trajectory
46
47       --vel  Write mapped velocities (if available)
48
49       --force
50              Write mapped forces (if available)
51
52       --hybrid
53              Create  hybrid  trajectory   containing   both   atomistic   and
54              coarse-grained
55
56
57       Mapping options:
58
59
60       --cg arg
61              coarse graining mapping and bond definitions (xml-file)
62
63       --map-ignore arg
64              list of molecules to ignore separated by ;
65
66       --no-map
67              disable mapping and act on original trajectory
68
69
70       Trajectory options:
71
72
73       --trj arg
74              atomistic trajectory file
75
76       --begin arg (=0)
77              skip frames before this time (only works for Gromacs files)
78
79       --first-frame arg (=0)
80              start with this frame
81
82       --nframes arg
83              process the given number of frames
84
85

AUTHORS

87       Written and maintained by the VOTCA Development Team <devs@votca.org>
88
89       This  Manual  Page  was converted from t2t format to the this format by
90       txt2tags (http://txt2tags.org) !   The  t2t  file  was  extracted  from
91       'csg_map --help' by help2t2t (version 2021 )
92

94       Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
95
96       Licensed under the Apache License, Version 2.0 (the "License"); you may
97       not use this file except in  compliance  with  the  License.   You  may
98       obtain a copy of the License at
99
100           http://www.apache.org/licenses/LICENSE-2.0
101
102       Unless  required  by  applicable  law or agreed to in writing, software
103       distributed under the License is distributed on an "AS IS" BASIS, WITH‐
104       OUT  WARRANTIES  OR  CONDITIONS OF ANY KIND, either express or implied.
105       See the License for the specific  language  governing  permissions  and
106       limitations under the License.
107
108
109
110
111Version: 2021                 2021-03-13 00:00:00                   csg_map(1)
Impressum