VMD-L Mailing List

From: Antonio Tilocca (a.tilocca_at_ucl.ac.uk)
Date: Fri Mar 07 2014 - 10:41:43 CST

I would like to use VMD to visualize all atoms X within 2A from another X.

Now, the command:

name X and within 2.0 of (name X)

always selects ALL X atoms in the system (not just those near to another
X) because, I guess, it always finds that the n-th atom of species X is
located at R=0A from itself.

I was wondering if there is an easy way to exclude from the distance
search the "self-interaction" between an atom and itself?

Thanks
Antonio