[gmx-users] Translation motion during MD

nahren manuel meetnahren at yahoo.com
Thu Nov 11 16:50:11 CET 2010

Dear Gromacs Users,

Yes Justin I totally agree with you and your point is well taken.  But given the fact that if i dont restrain the protein, they rotate and I dont get the formation of clusters.

Yes, i do want to protein to rotate in the plane of the membrane, but 
not the rotation that membrane-proximal become membrane -distal (this flipping rotation, if I may call like that)

Another alternate I was thinking was to do a steered MD, but since there is no clue which part (which domain in the protein) form cluster, this method doesn't help either.

Is  applying semiisotropic pressure a good idea ? similar to what one would do in membrane simulation.


--- On Thu, 11/11/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Translation motion during MD
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Thursday, November 11, 2010, 4:14 PM

nahren manuel wrote:
> Dear Gromacs Users,
> I am simulating a Membrane protein, the extracellular domain alone (since the structure of only extracellular domain is solved). So I will have to simulate the protein in such a way that only the translational motion is allowed but the rotational motions are prevented (which would mimic the behavior of the protein attached to the membrane).

I don't understand how you conclude that your protein shouldn't rotate.  Even if the transmembrane portion was there, the protein could certainly rotate in the plane of the membrane.

> The protein is expected to former dimer and multimers on the cell surface, so I want to restrict motion only to 2D. This would give an idea as to how the protein clusters on the membrane surface (studying this multimerization looks too ambitious, but want to make an attempt).

I suppose you could place a weak position restraint on all atoms in the z-dimension only.  I would seriously question the validity of doing so, though.  If you force a system into a preconceived behavior that masks other missing information, I'd say you're just causing the events to happen, not allowing them to occur naturally.  You're also causing unnatural forces between the membrane and the protein.  If the membrane deforms or undulates, the protein cannot accommodate this change.  This is true no matter how you restrict this 2-D motion, and I think it would be a serious problem.


> Best,
> nahren

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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