[gmx-users] Force-field bias???
jalemkul at vt.edu
Wed Aug 5 13:32:02 CEST 2015
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
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
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