[gmx-users] PMF calculation by umbrella sampling simulations
jalemkul at vt.edu
Thu Apr 30 23:20:37 CEST 2015
On 4/30/15 4:12 PM, MPI wrote:
> Hi Justin,
> Thanks for your explanation.
> In the tutorial, then what is a good approximate value of free energy
> ? if one follows the protocol. Is -37 or so kcal mol^-1 ?
That is what you should get from the tutorial.
> Here, 26 windows of COM distances are used, each for 10 ns simulation.
> In your original paper, -50.5 kcal mol^-1 is the free energy for
> dissociation of a single peptide from protofibril.
> In this full preparation, you used 31-window setup, each for 10 ns simulation.
> I've been aware of the difference between 26 and 31 windows but questions are
> First, if one obtains a reasonable histogram like
> ,how can one tell whether if the system needs more windows ?
> because these overlap windows look appropriate.
Simply looking at histograms only tells you if you're in the ballpark. g_wham
has a very nice set of options for doing error analysis. You'll note there is
minimal overlap in a few of your windows; these would correspond to regions of
the reaction coordinate with large error. If you do the bootstrap analysis you
will see this.
> Second, after full preparation, how did you know the free energy of
> -50.5 or so is a GOOD value ?
I did error analysis :) See details in the paper.
> Third, comparing a coarse ( the tutorial) with a full preparation (
> your original paper), it is somehow unclear that the number of
> windows can cause a significant difference of 13 kcal mol^-1 since
> it runs independently for 10 ns in each window.
> Please see PMF curve attached in a simulation of 26 windows, each for 10 ns.
> The PMF curve looks reasonable except when it converges to 37.5 kcal
> mol^-1 or so.
There is no clear energy minimum there and you haven't done error analysis, so
"looks good" doesn't really mean anything.
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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