Using gmx spatial?

User discussions
1

GROMACS version: 2020
GROMACS modification: No
How it is supposed to be used? The available description in the manual is rather curt.

So I have an unbiased MD trajectory of a nucleic acid in water. After a few attempts with trjconv visualizing it in PyMOL clearly shows that some solvent ions tend to linger at specific points.
Trying to adapt the listed example (using xtc instead of specified (why?) .tng (otherwise it results in error) and uppping the -nab value to 500) produces a sphere of small white dots in VMD centered on the solute.
How to get " the pictures are pretty and very informative " promised result? Filter out the non-persistent ones, color by occupancy, or something like that?

Or is that a legacy tool and there is some better way to display ion distribution?

2

Hi shelved,

You can give MPTG Computational Biophysics - Camilo Aponte-Santamaría a shot; the resulting density files can be visualised with pymol, vmd and chimera and should give you a wide range of neat visualisations.

I agree that this is a legacy tool that had not seen an upgrade in quite some time; thanks for posting this on the forum, it helps steering development effort to things that are afterthought.

3

@cblau
Thank you for suggestion. Will probably
For now I managed to get some result with gmx_spatial close enough for a figure.