csg_map man page

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

-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 <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 )

Info

Sun Feb 12 03:14:59 UTC 2017 Version: 1.4