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_rc1 )


Version: 1.4_rc1 Tue Oct 4 05:03:55 UTC 2016