csg_density(1) 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::

--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 <[email protected]>

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 1.3 )


Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at


Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.