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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.