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g_spatial_d

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

gromacs(7), g_sdf(1)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at http://www.gromacs.org/.