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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 se-
       lection	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 gmx trjconv 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 com-
	     pact -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	 clus-
       ter 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  op-
       tion  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 re-
       gion 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.

   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 suf-
       ficiently  high	value since memory is allocated	for cube bins based on
       the initial coordinates 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

       -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
	      reduce 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
	 suggesting the	use of the -nab	(Number	of Additional Bins) option  or
	 increasing the	-nab value.

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2025, GROMACS development team

2025.0				 Feb 10, 2025			GMX-SPATIAL(1)

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