gmx spatial#

Synopsis#

gmx spatial [-s [<.tpr/.gro/...>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
            [-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:

Use gmx make_ndx to create a group containing the atoms around which you want the SDF

gmx trjconv -s a.tpr -f a.tng -o b.tng -boxcenter tric -ur compact -pbc none

gmx trjconv -s a.tpr -f b.tng -o c.tng -fit rot+trans

run gmx spatial on the c.tng output of step #3.

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.

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 files:

-s [<.tpr/.gro/…>] (topol.tpr): Structure+mass(db): tpr gro g96 pdb brk ent
-f [<.xtc/.trr/…>] (traj.xtc): Trajectory: xtc trr cpt gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Optional): Index file

Other options:

-b <time> (0): Time of first frame to read from trajectory (default unit ps)
-e <time> (0): Time of last frame to read from trajectory (default unit ps)
-dt <time> (0): Only use frame when t MOD dt = first time (default unit 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> (16): Number of additional bins to ensure proper memory allocation

Known Issues#

When the allocated memory is not large enough, an error may occur suggesting the use of the -nab (Number of Additional Bins) option or increasing the -nab value.