Re: System Drifts Along Z-Axis

From: Bassam Haddad (
Date: Sun May 31 2020 - 16:16:52 CDT

Hi Peter,

Thank you for the detailed explanation, I see what you are saying. I am
having trouble getting a voltage across the membrane to converge, and
thought this drift to contribute to it.

I will use the colvars module as you have suggested, though I will continue
to search for the source of the issue - assuming it is more than a sampling

Thank you again for your explanation!


On Sun, May 31, 2020 at 1:32 PM Peter Freddolino <> wrote:

> Hi Bassam,
> My main point is that one has to be careful in thinking about the 'above'
> and 'below' solutions as separate, because they are topologically
> connected. That's not a problem if you're mostly interested in simulating a
> potential across a membrane, but is a problem if you expect to be able to
> think about the bulk solutions above/below it as independent of each other.
> I am pretty sure that based on the work of folks like JC who contribute
> regularly to this list (which you cited), the potential across the membrane
> will be independent of the diffusion of the membrane up or down in the unit
> cell, as long as you don't run into an extreme case where the membrane
> moved so far that there was no effective bulk electrolyte on one side of it
> or the other - outside of that extreme, the potential drop across the
> membrane for an electric field *E* will be *E* (dot) Lz (so mind that you
> keep the z dimension fixed unless you want the voltage across the membrane
> changing over time). You shouldn't expect the center of mass of the
> membrane (or any other degree of freedom) to remain fixed unless you do
> something to make it so; I don't think there's anything particularly
> surprising about the drift that you're seeing; it should be no more
> surprising than seeing a soluble protein diffuse around the simulation box
> rather than stay centered over the course of a simulation. Of course you
> could gently restrain the z coordinates or center of mass of the membrane
> and/or protein (perhaps using the colvars module) to remove any such risk--0000000000002d134f05a6f83316--

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