From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun May 31 2020 - 16:25:07 CDT
Hello Bassam, one other option to try is zeroMomentum:
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node35.html#11489
Read the corresponding doc to see if this is appropriate/beneficial for
your case.
Giacomo
On Sun, May 31, 2020 at 5:19 PM Bassam Haddad <bhaddad_at_pdx.edu> wrote:
> 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
> problem.
>
> Thank you again for your explanation!
>
> Best,
> Bassam
>
> On Sun, May 31, 2020 at 1:32 PM Peter Freddolino <petefred_at_umich.edu>
> 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
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Research collaborator, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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