csg_fluctuations1

Usage

Overview

calculate density fluctuations in subvolumes of the simulation box.Subolumes can be either cubic slabs in dimensions (x|y|z) or sphericalslabs with respect to either the center of box or a reference molecule

Options

Allowed options:

-h [ --help ] display this help and exit
--verbose be loud and noisy
--verbose1 be very loud and noisy
-v [ --verbose2 ] be extremly loud and noisy
--top arg atomistic topology file

Fluctuation options:

--filter arg (=*) filter molecule names
--rmax arg maximal distance to be considered
--rmin arg (=0) minimal distance to be considered
--refmol arg Reference molecule
--nbin arg (=100) Number of bins
--geometry arg (sphere|x|y|z) Take radial or x, y, z
slabs from rmin to rmax
--outfile arg (=fluctuations.dat) Output file

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