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
- -v [ --verbose ]
- be 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 <[email protected]>
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 1.3 )
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.