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
21       selection 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 which
31          you want the SDF
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33       2. gmx trjconv -s a.tpr -f a.tng -o b.tng -boxcenter tric  -ur  compact
34          -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
48       option 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
51       region  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> (4)
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, a segmentation fault
109         may occur. This is usually detected and the program is  halted  prior
110         to the fault while displaying a warning message suggesting the use of
111         the -nab (Number of Additional Bins)  option.  However,  the  program
112         does  not  detect  all  such  events. If you encounter a segmentation
113         fault, run it again with an increased -nab value.
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SEE ALSO

116       gmx(1)
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118       More    information    about    GROMACS    is    available    at     <‐
119       http://www.gromacs.org/>.
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COPYRIGHT

122       2019, GROMACS development team
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1272019.2                           Apr 16, 2019                   GMX-SPATIAL(1)