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

       VERSION 4.0.1


       g_densmap  -f  traj.xtc -s topol.tpr -n index.ndx -o densmap.xpm -[no]h
       -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 -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.

       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

       -o densmap.xpm Output
        X PixMap compatible matrix file


        Print help 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

       -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

                                Thu 16 Oct 2008                   g_densmap(1)