g_spatial(1)
NAME
g_spatial - calculate spatial distribution function
SYNOPSIS
g_spatial -s topol.tpr -f traj.xtc -n index.ndx -[no]h -nice int -b
time -e time -dt time -[no]w -[no]pbc -[no]div -ign int -bin real -nab
int
DESCRIPTION
g_nmtraj calculates the spatial distribution function (SDF) 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 32K atoms
and a 50ns trajectory, the SDF can be generated in about 30 minutes,
with most of the time dedicated to the two runs through trjconv(1) 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.
OPTIONS
- -s topol.tpr
- Structure+mass(db) (Input): tpr tpb tpa gro g96 pdb xml
- -f traj.xtc
- Generic trajectory (Input): xtc trr trj gro g96 pdb
- -n index.ndx
- Index file (Input, Output)
- -[no]h Print help info and quit (default: no).
- -nice int
- Set the nicelevel (default: 19).
- -b time
- First frame (ps) to read from trajectory (default: 0).
- -etime Last frame (ps) to read from trajectory (default: end of file).
- -[no]w View outpot xvg, xpm, eps, and pdb files (default: no).
- -[no]pbc
- Use periodic boundary conditions for computing distances (default: no).
- -[no]div
- 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 (default: TRUE).
- -ign int
- Do not display this number of outer cubes. Positive values may reduce boundary speckles; -1 ensures outer surface is visible (default: -1).
- -bin real
- Width of the bins in nm (default: 0.05).
- -nab int
- Number of additional bins to ensure proper memory allocation (default: 4).
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: Systems such as micelles will require micelle clustering 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). 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.
To reduce the amount of space and time required, you can output only
the coordinates 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 (Number of Additional Bins) option
value.
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
option. However, the program does not detect all such events. If you
encounter a segmentation fault, run it again with an increased -nab
value.
ALTERNATIVES
g_sdf also produces spatial distribution functions. g_spatial differs
from g_sdf in that g_spatial gives the user full control of the alignment procedure. The downside is that g_spatial requires more time and
more disk space.
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at http://www.gromacs.org/.