[gmx-users] PMF calculation by umbrella sampling simulations
jalemkul at vt.edu
Thu Apr 30 14:45:28 CEST 2015
On 4/30/15 12:43 AM, MPI wrote:
> Dear Users,
> With GMX 4.6.5, I tried to reproduce a system of the dissociation of
> a single peptide in an AB42 protofibril with PMF (potential of mean
> force) calculation in Justin's umbrella sampling tutorial. He
> derived the binding energy from PMF from a series of umbrella sampling
> simulations and obtained a value of free energy close to -50.5
> kcal mol-1. But I got a value of -37.5 kcal mol-1 after PMF
> curve was converged. The value difference is significant and this
> raises two questions. What dose cause this difference of ~13 kcal mol
> -1 ? although I used GPU for calculations, which is the only
> modification (cutoff-scheme = Verlet). What is a reasonable range of
> binding free energy in this case of AB42 protofibril ?
As I state in the tutorial and as I have said multiple times on the list (even
just a few days ago!), you will not produce the PMF profile shown in the
tutorial unless you follow the exact protocol in the paper (which is linked in
the tutorial). The value of -37 or so is what you will achieve if you do what
the tutorial says, which is a "quick and dirty" approximation of the protocol.
The full preparation (100 ns of MD on the protofibril, followed by a special
window setup described in the paper to adequately sample small COM distances)
will yield the quoted value.
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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