NAME

csg_fluctuations - Part of the VOTCA package

SYNOPSIS

csg_fluctuations [OPTIONS]

csg_fluctuations [–help]

DESCRIPTION

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