[gmx-users] Usage of g_spatial

[Justin Lemkul]

On 6/12/15 11:35 PM, V.V.Chaban wrote:
> 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?
>

Yes.  What you've shown below calculates the SDF of Li around water, the 
opposite of what you want.  The "solute" in this case should be the ion.

-Justin

>
>
>                              :-)  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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================