[gmx-users] Translation motion during MD
Justin A. Lemkul
jalemkul at vt.edu
Thu Nov 11 17:22:55 CET 2010
nahren manuel wrote:
> 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.
If you know the manner in which the clusters should form, then isn't this just a
problem of poor initial orientation?
> 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)
This sounds like a problem. If you have an ectodomain with a known structure,
then the transmembrane portion shouldn't be too complex, right? If there's an
anchoring transmembrane helix, it is trivial to construct and add onto the
> 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.
I guess this rebuts my comment above...
> Is applying semiisotropic pressure a good idea ? similar to what one
> would do in membrane simulation.
I don't see why not. Membranes should deform independently in x/y and z, so
semiisotropic is fine.
> --- 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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