g_spatial(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_spatial(1)

NAME

       g_spatial - calculates the spatial distribution function

       VERSION 4.5.4-dev-20110404-bc5695c

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 -center 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). There-
       fore 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 in 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 4 Apr 2011						      g_spatial(1)