shifting of ions from -z to +z in a single frame(1ps)

From: Basanta Acharya (
Date: Tue Oct 06 2020 - 21:54:07 CDT

Dear NAMD 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

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