[gmx-users] Usage of g_spatial

[V.V.Chaban]

Please, anyone comment on the correct usage of g_spatial.

I need a distribution of a solvation shell around an ion.

Do I choose the solvent as the first group (i.e. all atoms belonging
to the solvent) and the ion as the second group?



                            :-)  g_spatial_mpi  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -s         md.pdb  Input        Structure+mass(db): tpr tpb tpa gro g96 pdb
  -f         md.pdb  Input        Trajectory: xtc trr trj gro g96 pdb cpt
  -n      index.ndx  Input, Opt!  Index file

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-b           time   0       First frame (ps) to read from trajectory
-e           time   0       Last frame (ps) to read from trajectory
-dt          time   0       Only use frame when t MOD dt = first time (ps)
-[no]w       bool   no      View output .xvg, .xpm, .eps and .pdb files
-[no]pbc     bool   no      Use periodic boundary conditions for computing
                            distances
-[no]div     bool   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    100     Number of additional bins to ensure proper memory
                            allocation


WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

Select group to generate SDF:
Group     0 (         System) has    61 elements
Group     1 (          Other) has    61 elements
Group     2 (            MOL) has    61 elements
Group     3 (             LI) has     1 elements
Group     4 (             O*) has    20 elements
Group     5 (             H*) has    40 elements
Group     6 (          H*_O*) has    60 elements
Select a group: 3
Selected 3: 'LI'
Select group to output coords (e.g. solute):
Group     0 (         System) has    61 elements
Group     1 (          Other) has    61 elements
Group     2 (            MOL) has    61 elements
Group     3 (             LI) has     1 elements
Group     4 (             O*) has    20 elements
Group     5 (             H*) has    40 elements
Group     6 (          H*_O*) has    60 elements
Select a group: 6
Selected 6: 'H*_O*'
Reading frame       0 time    1.000    '', 61 atoms
Reading frame     900 time    1.000