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


       g_spatial - calculates the spatial distribution function

       VERSION 4.6.5


       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


        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.


       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


       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.


       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.


       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.


       -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


        Print help info and quit

        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)

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

        Use periodic boundary conditions for computing distances

        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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                             g_spatial(1)