NAME

csg_map - Part of the VOTCA package

SYNOPSIS

csg_map [OPTION] [OPTIONPARAMETERS]

DESCRIPTION

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). Examples: * 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

Please visit the program site at __http://www.votca.org__.

OPTIONS

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

AUTHORS

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

This Manual Page was converted from t2t format to the this format by txt2tags (http://txt2tags.org) ! The t2t file was extracted from 'csg_map --help' by help2t2t (version 1.6.4 )

COPYRIGHT

Copyright 2009-2011 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.