billy.williams-noonan at monash.edu
Thu Nov 10 04:06:32 CET 2016
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
some mathematical tool that can tell you the likelihood that the entire
conformational space has been sampled adequately?
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
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Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon
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