System Drifts Along Z-Axis

From: Bassam Haddad (
Date: Fri May 29 2020 - 14:36:49 CDT

Hello NAMDers,

I noticed that when I am running my simulation of a membrane-bound channel
that the whole system (membrane + protein) drifts along the z-axis,
effectively altering the volume of the bulk solutions above and below the
membrane. My goal is to run an external electric field simulation and need
the volume of the bulk solutions to remain constant to allow the system to
develop a reaction field.

Someone had mentioned that I might have chosen the wrong thermostat, and
have excess energy leaking during the equilibrium simulation. I am
currently using Langevin dynamics for my temperature control. They had
mentioned known errors <> with
the Barendsen thermostat, but I am not certain if that is the issue in my

I am curious if anyone has experienced this issue, either in general or in
regard to an externally applied force simulation. Attached is my
equilibration configuration file for reference.

Thank you!


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