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).
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
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