[gmx-users] The Rationality of Position Restrain in Umbrella Sampling

[Justin Lemkul]

On 5/2/17 10:34 AM, Jason Zhu wrote:
> Dear Justin,
>
> Thank you for your prompt response. Your information is very helpful.
>
> Now I understand that the position restrain is used to to mimic the
> stability of a much larger structure of A-beta fibrils and make the pulling
> direction coincident with the fibril axis.
>
> The system I am studying is a complex of two same molecules (in linear
> shapes). I tried to separate them and calculate the binding free energy. My
> question is whether the free energy or energy curve is dependent of pulling
> direction with respect to the complex orientation. If I removed the
> position restrain, the two linear molecules preferred to rotate first until
> their interface parallel to the pulling direction and slide away from each
> other. Is it reasonable and valid to get the correct binding free energy
> and energy curve? Do I need change the initial orientation to the preferred
> one?
>

Sufficiently long simulations should determine the conformational preferences. 
Adequate sampling of orthogonal degrees of freedom is needed no matter what you 
do.  But your case is simple in that you should just define the bias between the 
COM of each molecule and let them sample whatever ensemble they sample.

-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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