gmx-spatial(1) GROMACS Manual gmx-spatial(1)NAMEgmx-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 sys‐
tem 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 rotat‐
ing 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 sug‐
gesting the use of the -nab (Number of Additional Bins) option. How‐
ever, 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 out‐
put only the coords that are going to be used in the first and subse‐
quent 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-spatial(1)
