From: Axel Kohlmeyer (
Date: Tue Oct 06 2020 - 22:13:37 CDT

This sounds like periodic boundary conditions at work. Nothing to worry

On Tue, Oct 6, 2020 at 11:01 PM Basanta Acharya <>

> Dear VMD users,
> I had set the cell basis vectors for my system (carbon nanotube having
> water box on both ends, and a water box at one end contains some ions) by
> measuring the size of the system and then minimized the system and ran the
> equilibration. When equilibration starts, after some times I observed that
> some ions moved from -z to +z in a single frame (1ps). How can I solve it ?
> I think this is because of the cell basis vectors, if not please let me
> know the reason behind it. Thank you !
> With best regards,
> Basanta Acharya
> M.SC. Physics
> Tribhuvan University
> email:

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.