From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Sun May 31 2020 - 14:09:37 CDT
That’s a great point, and one that I will try to address.
When doing a constant electric field simulation, including a periodic
boundary, the water and ions in each bath should re-orient to create a
reaction field against the externally applied one. What then arises is a
constant potential above and below the membrane that are separated by some
voltage (V = E*L) across the membrane. My understanding is that the volumes
should remain more or less constant to have a well behaved voltage drop
(see attachment). Perhaps my understanding is a bit misguided, would the
drift not cause any issues during a constant E-Field simulation?
On Sun, May 31, 2020 at 11:33 AM Peter Freddolino <petefred_at_umich.edu>
> 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
>> 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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