jalemkul at vt.edu
Thu Nov 10 16:51:35 CET 2016
On 11/9/16 10:06 PM, Billy Williams-Noonan wrote:
> Hey Justin, out of interest, when the PMF flattens at the end (the rate of
> change is zero), how do we know that the PMF has truly converged? Is there
Reaching a plateau says nothing about the convergence of the PMF, that's just an
expected result that you'll see even in a badly converged one, based on how the
WHAM algorithm works.
> some mathematical tool that can tell you the likelihood that the entire
> conformational space has been sampled adequately?
No simulation ever samples the entire conformational space. What needs to be
shown is that an adequate amount of the conformational space has been sampled,
sufficient to converge the observables of interest and answer whatever the
underlying question is. There are lots of opinions on this in terms of what
constitutes convergence, in terms of the PMF and other physical quantities from
the simulation, it should show no time-dependence. Then, you need to figure out
if your molecule(s) of interest gave you enough dynamics to actually be reliable.
> On 10 November 2016 at 13:44, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 11/9/16 2:54 PM, m g wrote:
>>> Dear Justin Lemkul,You said "The PMF itself (being the primary output of
>>> umbrella sampling) is a good start." for checking the convergence. what did
>>> you mean? I was obtained PMF, did you mean that we check the overlap of
>>> histogram of configurations?
>> Ask yourself: how would you check convergence of any quantity? What does
>> "convergence" mean?
>> 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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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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