csg_density man page

csg_density — Part of the VOTCA package




Calculates the mass density distribution along a box axis or radial density profile from reference point

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

Mapping options:

--cg arg

[OPTIONAL] coarse graining mapping and bond definitions (xml-file). If no file is given, program acts on original trajectory

--map-ignore arg

list of molecules to ignore if mapping is done separated by ;

Specific options::

--type arg (=mass)

density type: mass or number

--axis arg (=r)

[x|y|z|r] density axis (r=spherical)

--step arg (=0.01)

spacing of density

--block-length arg

write blocks of this length, the averages are cleared after every write

--out arg

Output file

--rmax arg

rmax (default for [r] =min of all box vectors/2, else l )

--scale arg (=1)

scale factor for the density

--molname arg (=*)


--filter arg (=*)

filter bead names

--ref arg

reference zero point

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_density --help' by help2t2t (version 1.4 )


Sun Feb 12 03:14:54 UTC 2017 Version: 1.4