1GMX-SPATIAL(1)                      GROMACS                     GMX-SPATIAL(1)
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NAME

6       gmx-spatial - Calculate the spatial distribution function
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SYNOPSIS

9          gmx spatial [-s [<.tpr/.gro/...>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
10                      [-b <time>] [-e <time>] [-dt <time>] [-[no]w] [-[no]pbc]
11                      [-[no]div] [-ign <int>] [-bin <real>] [-nab <int>]
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DESCRIPTION

14       gmx spatial calculates the spatial distribution function and outputs it
15       in a form that can be read by VMD as Gaussian98  cube  format.   For  a
16       system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated
17       in about 30 minutes, with most of the time dedicated to  the  two  runs
18       through  trjconv that are required to center everything properly.  This
19       also takes a whole bunch of space (3 copies of  the  trajectory  file).
20       Still, the pictures are pretty and very informative when the fitted se‐
21       lection is properly made.  3-4 atoms in a widely mobile group  (like  a
22       free amino acid in solution) works well, or select the protein backbone
23       in a stable folded structure to get the SDF of solvent and look at  the
24       time-averaged  solvation shell.  It is also possible using this program
25       to generate the SDF based on some arbitrary Cartesian coordinate. To do
26       that, simply omit the preliminary gmx trjconv steps.
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28       Usage:
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30          1. Use  gmx  make_ndx  to create a group containing the atoms around
31             which you want the SDF
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33          2. gmx trjconv -s a.tpr -f a.tng -o b.tng -boxcenter tric  -ur  com‐
34             pact -pbc none
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36          3. gmx trjconv -s a.tpr -f b.tng -o c.tng -fit rot+trans
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38          4. run gmx spatial on the c.tng output of step #3.
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40          5. Load grid.cube into VMD and view as an isosurface.
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42       Note  that systems such as micelles will require gmx trjconv -pbc clus‐
43       ter between steps 1 and 2.
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45   Warnings
46       The SDF will be generated for a cube that contains all bins  that  have
47       some  non-zero  occupancy.  However, the preparatory -fit rot+trans op‐
48       tion to gmx trjconv implies that  your  system  will  be  rotating  and
49       translating  in  space  (in  order  that  the selected group does not).
50       Therefore the values that are returned will only be valid for some  re‐
51       gion  around  your  central group/coordinate that has full overlap with
52       system volume throughout the entire translated/rotated system over  the
53       course  of the trajectory.  It is up to the user to ensure that this is
54       the case.
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56   Risky options
57       To reduce the amount of space and time required, you  can  output  only
58       the  coords  that  are going to be used in the first and subsequent run
59       through gmx trjconv.  However, be sure to set the -nab option to a suf‐
60       ficiently  high  value since memory is allocated for cube bins based on
61       the initial coordinates and the -nab option value.
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OPTIONS

64       Options to specify input files:
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66       -s [<.tpr/.gro/...>] (topol.tpr)
67              Structure+mass(db): tpr gro g96 pdb brk ent
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69       -f [<.xtc/.trr/...>] (traj.xtc)
70              Trajectory: xtc trr cpt gro g96 pdb tng
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72       -n [<.ndx>] (index.ndx) (Optional)
73              Index file
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75       Other options:
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77       -b <time> (0)
78              Time of first frame to read from trajectory (default unit ps)
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80       -e <time> (0)
81              Time of last frame to read from trajectory (default unit ps)
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83       -dt <time> (0)
84              Only use frame when t MOD dt = first time (default unit ps)
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86       -[no]w (no)
87              View output .xvg, .xpm, .eps and .pdb files
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89       -[no]pbc (no)
90              Use periodic boundary conditions for computing distances
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92       -[no]div (yes)
93              Calculate and apply the divisor for  bin  occupancies  based  on
94              atoms/minimal  cube  size.  Set as TRUE for visualization and as
95              FALSE (-nodiv) to get accurate counts per frame
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97       -ign <int> (-1)
98              Do not display this number of outer cubes (positive  values  may
99              reduce boundary speckles; -1 ensures outer surface is visible)
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101       -bin <real> (0.05)
102              Width of the bins (nm)
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104       -nab <int> (16)
105              Number of additional bins to ensure proper memory allocation
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KNOWN ISSUES

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

113       gmx(1)
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115       More     information    about    GROMACS    is    available    at    <‐
116       http://www.gromacs.org/>.
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119       2022, GROMACS development team
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1242022.3                           Sep 02, 2022                   GMX-SPATIAL(1)
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