[gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

Justin Lemkul jalemkul at vt.edu
Thu Sep 29 16:59:54 CEST 2016

On 9/29/16 5:05 AM, Erik Marklund wrote:
> Hi,
> 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,
> Erik
>> 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 and
>> 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.
>> Regards,
>> Abhishek Acharya
>> --
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.


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


More information about the gromacs.org_gmx-users mailing list