[gmx-users] Free energy - Methane in water
jalemkul at vt.edu
Thu May 19 03:14:42 CEST 2016
On 5/18/16 6:46 AM, Alexander Alexander wrote:
> Dear gromacs user,
> In Free energy calculation tutorial of Methane in water, two energy
> minimization steps are done in order, first the steepest descents one where the
> rigid structures are used and then L-BFGS in which the flexible structure
> is used in (define = -DFLEXIBLE).
> My question is: in a two-steps minimization in general if it make sense to
> apply a rigid structure first and then to apply flexible structure
You may have to re-minimize with constraints in complex systems or ones in which
significant X-H bond stretching occurs as a result. But for a trivial system
like the tutorial, there should be no bizarre behavior.
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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