VMD-L Mailing List

From: Amir (amirsuhail029us_at_gmail.com)
Date: Sun Feb 18 2024 - 14:54:49 CST

Dear all,

I am doing some calculations on the Lammps trajectory, for which I need to
find all information of neighbors within a cutoff around every bead. My
code works fine for all the polymers (bead-spring model), which are well
within the box. I am finding neighbors around a bead as follows:

set sel [atomselect top “within 3 of index 10”]

Suppose my bead (say index 10) is at the edge of the box, and the polymer
and some other chains are crossing the boundary and appearing from the
other side. This atom selection is not capturing all the neighbors,
considering periodic boundaries. It is only giving me the beads around the
edge, not from the other side, which are within cutt-off of my bead of
interest considering periodic boundaries. Is there a way to get all the
neighbors for edges? Thank you in advance.

Best regards,
Amir