Provided by: gromacs-data_2018.1-1_all bug


       gmx-spatial - Calculate the spatial distribution function


          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>]


       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.


       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.

       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 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> (4)
              Number of additional bins to ensure proper memory allocation


       · 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 (Number of Additional Bins) option. However,  the
         program  does  not detect all such events. If you encounter a segmentation fault, run it
         again with an increased -nab value.



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       2018, GROMACS development team