[gmx-users] Translation motion during MD

[Justin A. Lemkul]

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
> 
> 
> 
> 
> 
> 
> 

-- 
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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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