NAME¶

csg_map - Part of the VOTCA package

SYNOPSIS¶

csg_map [OPTIONS]

csg_map [--help]

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).
* 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

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>

COPYRIGHT¶

Copyright 2009-2024 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.