From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun May 31 2020 - 13:35:00 CDT
I'm confused as to part of the premise here. If you're using periodic
boundary conditions, why do you think that 'above' and 'below' the membrane
are different?
On Fri, May 29, 2020 at 4:38 PM Bassam Haddad <bhaddad_at_pdx.edu> wrote:
> 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 <https://en.wikipedia.org/wiki/Flying_ice_cube> with
> the Barendsen thermostat, but I am not certain if that is the issue in my
> case.
>
> 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!
>
> Bassam
>
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