1csg_map(1) General Commands Manual csg_map(1)
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6 csg_map - Part of the VOTCA package
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10 csg_map [OPTION] [OPTIONPARAMETERS]
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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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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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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 )
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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 2019-02-17 00:15:52 csg_map(1)