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

[Smith, Micholas D.]

You should also note that force-field bias may be system dependent. So if you are unsure of the dynamics from the onset, you should likely test a variety of force-fields and/or try to find a comparison to NMR (or other) experimental methods.

-Micholas

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Wednesday, August 05, 2015 7:31 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Force-field bias???

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

--
==================================================

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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