[gmx-users] about position restrain

[Justin Lemkul]

On 8/19/16 2:40 PM, Albert wrote:
> Hello:
>
> I built a homology model for membrane protein MD simulation. I would like to
> restrain the backbone of the protein. However, I am going to study the
> dimerization of this protein and I don't want to restrain the drifting of this
> protein, otherwise they would never forms a dimer spontaneously.
>
> According to my experiences, if we add position restrain to the protein
> backbone, probably the overall protein will stay in the same place forever. It
> won't drift to somewhere else.
>
> I am just wondering what we can do?
>

Why is it necessary to impose any restraint on the backbone in the first place? 
If you don't have confidence in the homology model and you are enforcing a given 
structure, then there is little confidence that any observed dimerization is 
legitimate.  You should prove that the structure is reasonable/stable and do a 
normal simulation without restraints.

If, for some reason, you must apply restraints to maintain some secondary 
structure element(s), then use dihedral restraints, not position restraints.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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