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From: SHIVAM TIWARI (t.shivam_at_iitg.ac.in)
Date: Mon Feb 19 2024 - 00:41:43 CST

I am not sure though, but unwrapping the trajectory and then doing the analysis may get the desired result.

Just type : "pbc unwrap" in the tkconsole after loading your trajectory to unwrap.

Regards,
Shivam

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From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Amir <amirsuhail029us_at_gmail.com>
Sent: Monday, February 19, 2024 2:24:49 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: atomselection near periodic boundaries

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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