[gmx-users] Translation motion during MD
Justin A. Lemkul
jalemkul at vt.edu
Thu Nov 11 16:14:48 CET 2010
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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