[gmx-users] Free energy - Methane in water

[Justin Lemkul]

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
> afterward?
>

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

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

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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