From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Sun May 31 2020 - 16:56:05 CDT
Thank you, Giacomo!
I’ll certainly check it out.
Bassam
On Sun, May 31, 2020 at 2:25 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> 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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