[gmx-users] Non-overlapping region appears in histograms when using SMD+Umbrella Sampling for strong binding complex

Justin Lemkul jalemkul at vt.edu
Fri Apr 21 14:20:44 CEST 2017

On 4/20/17 3:40 PM, Jason Zhu wrote:
> Dear Justin,
> Thank you very much for your prompt response.
> It is really a good idea to get the desired structures by "setting the reference
> distance to the one you want, setting the pull rate to zero, and just letting
> the system equilibrate under the biasing potential". I will try what you suggest.
> Only one small question about the "SMD/PMF" you are referring to in the end of
> the letter. Is it the same method (SMD+Umbrella Sampling) I used, or calculating
> PMF directly by integrating the force in SMD? I also tried the latter one. But
> the result is dependent of the loading rate.

I mean to do what you were proposing - SMD followed by umbrella sampling to get 
the PMF.  The Jarzynski method for getting the PMF from SMD is indeed difficult 
to converge.



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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