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GMX-SPATIAL(1)			     GROMACS			  GMX-SPATIAL(1)

NAME
     gmx-spatial - Calculate the spatial distribution function

SYNOPSIS
	gmx spatial [-s [<.tpr/.gro/...>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
		    [-b <time>] [-e <time>] [-dt <time>] [-[no]w] [-[no]pbc]
		    [-[no]div] [-ign <int>] [-bin <real>] [-nab <int>]

DESCRIPTION
     gmx  spatial calculates the spatial distribution function and outputs it in
     a form that can be read by VMD as Gaussian98 cube format.	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 trajectory 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 arbi-
     trary Cartesian coordinate. To do that, simply omit the preliminary gmx tr-
     jconv steps.

     Usage:

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

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

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

	4. run gmx spatial on the c.tng output of step #3.

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

     Note  that  systems  such as micelles will require gmx 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 gmx
     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/coor-
     dinate 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.

   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
     gmx 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 co-
     ordinates and the -nab option value.

OPTIONS
     Options to specify input files:

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

     -f [<.xtc/.trr/...>] (traj.xtc)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

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

     -[no]pbc (no)
	    Use periodic boundary conditions for computing distances

     -[no]div (yes)
	    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 re-
	    duce boundary speckles; -1 ensures outer surface is visible)

     -bin <real> (0.05)
	    Width of the bins (nm)

     -nab <int> (16)
	    Number of additional bins to ensure proper memory allocation

KNOWN ISSUES
     * When the allocated memory is not large enough, an error	may  occur  sug-
       gesting	the  use  of  the -nab (Number of Additional Bins) option or in-
       creasing the -nab value.

SEE ALSO
     gmx(1)

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

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			  GMX-SPATIAL(1)
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