Provided by: gromacs-data_2019.3-2_all bug

NAME

       gmx-densmap - Calculate 2D planar or axial-radial density maps

SYNOPSIS

          gmx densmap [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                      [-od [<.dat>]] [-o [<.xpm>]] [-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>]

DESCRIPTION

       gmx  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.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/…>] (traj.xtc)
              Trajectory: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/…>] (topol.tpr) (Optional)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -od [<.dat>] (densmap.dat) (Optional)
              Generic data file

       -o [<.xpm>] (densmap.xpm)
              X PixMap compatible matrix file

       Other options:

       -b <time> (0)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -[no]w (no)
              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, 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

       -[no]mirror (no)
              Add the mirror image below the axial axis

       -[no]sums (no)
              Print density sums (1D map) to stdout

       -unit <enum> (nm-3)
              Unit for the output: nm-3, nm-2, count

       -dmin <real> (0)
              Minimum density in output

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

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2019, GROMACS development team