Ubuntu Manpage: gmx-spatial - Calculate the spatial distribution function

Provided by: gromacs-data_2023.3-1ubuntu3_all

NAME

       gmx-spatial - Calculate the spatial distribution function

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:

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 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.

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