VMD-L Mailing List

From: Bart Bruininks (b.m.h.bruininks_at_rug.nl)
Date: Fri Jun 05 2020 - 08:14:43 CDT

Dear VMDers,

I was trying to calculate contacts between molecules of the same species.
Usually the VMD selection procedure is very fast and accurate compared to
other options (GROMACS, MDAnalysis, etc). However, I can't seem to prevent
every molecule from returning True to the selection below:

resname X and pbwithin 8 of resname X

This makes sense, for X is a multiparticle molecule, therefore it is always
in range of itself. Is there something neat I can do to prevent this from
happening (preferably without affecting calculation time too much).

I did find something related about the 'gofr' module from 2008, but I am
not sure how relevant it is. Back then such a selection was not possible, I
wonder if this is still the case.

Cheers,

Bart