[gmx-users] Force-field bias???

[Justin Lemkul]

On 8/5/15 6:24 AM, SAPNA BORAH wrote:
> Dear all,
>
> I have a general query about unfolding simulations. Is there a bias among
> force-fields selected for unfolding, i.e. is it possible that unfolding of
> the protein may be different with a change in force fields applied?
> Literature has given some support on this, however, I am not sure how this
> may happen.
>

Yes, this is true.  It usually comes down to errors in the balance between 
intra-protein and protein-water interactions.  Incorrect balance favors either 
the folded or unfolded state.  No force field is perfect, but some are better 
than others and there's lots of literature on this topic regarding which are the 
most successful.

-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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