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
structure.
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.
-Justin
Best,
nahren
--- On *Thu, 11/11/10, Justin A. Lemkul /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] Translation motion during MD
To: "Discussion list for GROMACS users" <[email protected]>
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.
-Justin
> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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