[gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.
abhi117acharya at gmail.com
Fri Sep 30 03:35:02 CEST 2016
Thank you Eric and Justin for your suggestions. In that case, I will then
go for a single COM group for the whole system.
On Sep 29, 2016 20:30, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> On 9/29/16 5:05 AM, Erik Marklund wrote:
>> I don’t simulate membranes much, so perhaps someone else’s input might be
>> more valuable. But unless the relative motion of the membrane with respect
>> to the rest is artificial and not just diffusion, I would still recommend
>> COM-motion removal of the whole system.
> For interfacial systems, membranes, etc. it is common to remove COM motion
> of the different layers (membrane/water) separately because they have
> different diffusion properties. There are a few systematic studies of
> this, some rather old, that say it is necessary to avoid spurious
> contributions to lipid diffusion. IIRC the effects are rather small, but
> nonetheless easy to account for.
> Now, with proteins in the mix it becomes more complicated. If it's an
> integral membrane protein, I generally treat it as part of the membrane.
> In this case, it is a lot less clear what one should do, since there are
> multiple peptides and they are (as I understand it) peripherally bound and
> therefore interacting with the aqueous layer and lipids. This is a
> nontrivial problem, and probably treating the system as one group for COM
> removal is appropriate. The lipid diffusion may not be 100% correct, but
> depending on the aims of the study it may not be a significant factor.
> Kind regards,
>> On 28 Sep 2016, at 16:39, Abhi Acharya <abhi117acharya at gmail.com> wrote:
>>> Thank you Eric for your clarification. However, I have seen that in
>>> membrane simulations, its is suggested to couple membrane, and solvent
>>> solute to two different COM groups. The argument is that in case of
>>> membrane systems, there is an inherent tendency of lateral drift of
>>> membranes; with a single COM for the whole system, even though the COM
>>> would remain essentially unchanged, there may be appreciable drift of the
>>> membrane relative to the rest of the system. Could you possibly shed some
>>> light on this?
>>> Following the above argument, probably for my system I should assign
>>> membrane to one COM group and the rest of the system (including solute
>>> solvent and the peprides ) to other. What do you think?
>>> Thank you.
>>> Abhishek Acharya
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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