Provided by: gromacs-data_4.6.5-1build1_all bug


       g_densmap - calculates 2D planar or axial-radial density maps

       VERSION 4.6.5


       g_densmap  -f  traj.xtc  -s  topol.tpr  -n index.ndx -od densmap.dat -o densmap.xpm -[no]h
       -[no]version -nice int -b time -e time -dt time -[no]w -bin real  -aver  enum  -xmin  real
       -xmax  real  -n1  int -n2 int -amax real -rmax real -[no]mirror -[no]sums -unit enum -dmin
       real -dmax real


        g_densmap computes 2D number-density maps.  It can make planar and  axial-radial  density
       maps.   The  output  .xpm file can be visualized with for instance xv and can be converted
       to postscript with  xpm2ps.  Optionally, output can be in text form to a  .dat  file  with
       -od, instead of the usual  .xpm file with  -o.

       The  default analysis is a 2-D number-density map for a selected group of atoms in the x-y
       plane.  The averaging direction can be changed with the option  -aver.  When  -xmin and/or
       -xmax are set only atoms that are within the limit(s) in the averaging direction are taken
       into account.  The grid spacing is set with the  option   -bin.   When   -n1  or   -n2  is
       non-zero,  the  grid size is set by this option.  Box size fluctuations are properly taken
       into account.

       When options  -amax and  -rmax are set, an axial-radial number-density map is made.  Three
       groups  should  be  supplied, the centers of mass of the first two groups define the axis,
       the third defines the analysis group. The axial direction goes from -amax to +amax,  where
       the  center  is  defined  as  the  midpoint  between  the centers of mass and the positive
       direction goes from the first to the second center of mass.   The  radial  direction  goes
       from 0 to rmax or from -rmax to +rmax when the  -mirror option has been set.

       The  normalization  of  the  output is set with the  -unit option.  The default produces a
       true number density. Unit  nm-2 leaves out the normalization  for  the  averaging  or  the
       angular  direction.  Option  count produces the count for each grid cell.  When you do not
       want the scale in the output to go from zero to the  maximum  density,  you  can  set  the
       maximum with the option  -dmax.


       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input, Opt.
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -od densmap.dat Output, Opt.
        Generic data file

       -o densmap.xpm Output
        X PixMap compatible matrix file


        Print help info and quit

        Print version info and quit

       -nice int 19
        Set the nicelevel

       -b time 0
        First frame (ps) to read from trajectory

       -e time 0
        Last frame (ps) to read from trajectory

       -dt time 0
        Only use frame when t MOD dt = first time (ps)

        View output  .xvg,  .xpm,  .eps and  .pdb files

       -bin real 0.02
        Grid size (nm)

       -aver enum z
        The direction to average over:  z,  y or  x

       -xmin real -1
        Minimum coordinate for averaging

       -xmax real -1
        Maximum coordinate for averaging

       -n1 int 0
        Number of grid cells in the first direction

       -n2 int 0
        Number of grid cells in the second direction

       -amax real 0
        Maximum axial distance from the center

       -rmax real 0
        Maximum radial distance

        Add the mirror image below the axial axis

        Print density sums (1D map) to stdout

       -unit enum nm-3
        Unit for the output:  nm-3,  nm-2 or  count

       -dmin real 0
        Minimum density in output

       -dmax real 0
        Maximum density in output (0 means calculate it)



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                             g_densmap(1)