csg_map man page

csg_map — Part of the VOTCA package




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__.


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
Write mapped velocities (if available)
Write mapped forces (if available)
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 ;
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


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 1.4_rc1 )


Version: 1.4_rc1 Tue Oct 4 05:03:54 UTC 2016