Which tools for calculation of number of nonpolar contacts?

Hi gmx users,

With what command from Gromacs software can the parameter of Fig 1E (number of nonpolar contacts) of the following article be obtained?

Or the parameter of Fig 8 of the following paper (Occupancy of hydrophobic interaction in protein-ligand complex)

Biomolecules | Free Full-Text | Structural Basis for Vascular Endothelial Growth Factor Receptor Activation and Implications for Disease Therapy | HTML)?

Please guide me.

Hi,
I do not know in your specific case, but gmx mindist output the number of contact between one group and a number of other groups.
Best regards
Alessandra

Hi. Thanks Alessandra.

I used this command: gmx mindist -f md.xtc -s md.tpr -n index.ndx -d 0.6 -group

And I selected two groups. But I obtained only 1 output file (mindist.xvg) containing distance info and without info about number of contacts.

In the online manual, I saw:
gmx mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files.

How to resolve it?

You will need to use -on to get the output time series of contacts within your chosen groups.

Thanks Justin.
My problem was solved. Now, I have another question:

Based on manual, default distance for contacts is 0.6. Is this distance appropriate for evaluation of number of non-polar contact? Or should I choose another amount for -d ?

I think the default value comes from an approximation of the sum of van der Waals radii for generic atom types. You’d have to determine if such a value is reasonable, and I have no real insight as to whether it is, though I suspect it is fairly widely used.