NAME

       g_spatial - calculates the spatial distribution function

       VERSION 4.6.5

SYNOPSIS

       g_spatial  -s  topol.tpr  -f traj.xtc -n index.ndx -[no]h -[no]version -nice int -b time -e time -dt time
       -[no]w -[no]pbc -[no]div -ign int -bin real -nab int

DESCRIPTION

        g_spatial calculates the spatial distribution function and outputs it in a form that can be read by  VMD
       as  Gaussian98  cube  format.   This was developed from template.c (GROMACS-3.3).  For a system of 32,000
       atoms and a 50 ns trajectory, the SDF can be generated in  about  30  minutes,  with  most  of  the  time
       dedicated  to  the  two runs through  trjconv that are required to center everything properly.  This also
       takes a whole bunch of space (3 copies of the  .xtc file).  Still,  the  pictures  are  pretty  and  very
       informative  when the fitted selection is properly made.  3-4 atoms in a widely mobile group (like a free
       amino acid in solution) works well, or select the protein backbone in a stable folded  structure  to  get
       the SDF of solvent and look at the time-averaged solvation shell.  It is also possible using this program
       to generate the SDF based on some arbitrary Cartesian coordinate. To do that, simply omit the preliminary
       trjconv steps.

       USAGE:

       1. Use  make_ndx to create a group containing the atoms around which you want the SDF

       2.  trjconv -s a.tpr -f a.xtc -o b.xtc -boxcenter tric -ur compact -pbc none

       3.  trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans

       4. run  g_spatial on the  .xtc output of step 3.

       5. Load  grid.cube into VMD and view as an isosurface.

        Note that systems such as micelles will require  trjconv -pbc cluster between steps 1 and 2

       WARNINGS:

       The  SDF will be generated for a cube that contains all bins that have some non-zero occupancy.  However,
       the preparatory  -fit rot+trans option to   trjconv  implies  that  your  system  will  be  rotating  and
       translating  in space (in order that the selected group does not). Therefore the values that are returned
       will only be valid for some region around your central group/coordinate that has full overlap with system
       volume  throughout  the  entire translated/rotated system over the course of the trajectory.  It is up to
       the user to ensure that this is the case.

       BUGS:

       When the allocated memory is not large enough, a segmentation fault may occur. This is  usually  detected
       and the program is halted prior to the fault while displaying a warning message suggesting the use of the
       -nab (Number of Additional Bins) option. However, the program does not detect all  such  events.  If  you
       encounter a segmentation fault, run it again with an increased  -nab value.

       RISKY OPTIONS:

       To reduce the amount of space and time required, you can output only the coords that are going to be used
       in the first and subsequent run through  trjconv.  However,  be  sure  to  set  the   -nab  option  to  a
       sufficiently  high value since memory is allocated for cube bins based on the initial coordinates and the
       -nab option value.

FILES

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

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

       -n index.ndx Input, Opt.
        Index file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 0
        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)

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -[no]pbcno
        Use periodic boundary conditions for computing distances

       -[no]divyes
        Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set  as  TRUE  for
       visualization and as FALSE ( -nodiv) to get accurate counts per frame

       -ign int -1
        Do  not  display  this  number  of outer cubes (positive values may reduce boundary speckles; -1 ensures
       outer surface is visible)

       -bin real 0.05
        Width of the bins (nm)

       -nab int 4
        Number of additional bins to ensure proper memory allocation

SEE ALSO

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                     g_spatial(1)