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gmx-spatial(1)                  GROMACS Manual                  gmx-spatial(1)

NAME
       gmx-spatial - Calculate the spatial distribution function

SYNOPSIS
       gmx spatial [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]
                   [-n [<.ndx>]] [-nice <int>] [-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 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
       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/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 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 coordinates and the -nab option value.

OPTIONS
       Options to specify input and output files:

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

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

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

       Other options:

       -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]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> (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/>.

VERSION 5.0.6                                                   gmx-spatial(1)