table of contents
g_spatial(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_spatial(1) |
NAME¶
g_spatial - calculates the spatial distribution functionSYNOPSIS¶
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 intDESCRIPTION¶
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.FILES¶
-s topol.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb
Trajectory: xtc trr trj gro g96 pdb cpt
Index file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
Use periodic boundary conditions for computing distances
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
Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible)
Width of the bins in nm
Number of additional bins to ensure proper memory allocation
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |