[gmx-users] Umbrella Sampling and Histogram

Justin Lemkul jalemkul at vt.edu
Fri Feb 20 14:46:00 CET 2015

On 2/19/15 9:50 PM, Agnivo Gosai wrote:
> Dear Users
> This is my earlier post wherein I received useful suggestion from Dr.
> Lemkul.
> http://comments.gmane.org/gmane.science.biology.gromacs.user/74659
> Earlier for my system , I was doing a 1 ns Umbrella Sampling run for each
> window and my histogram looked like this :- ​
> <https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web>
>> Now, I , kept all other stuff ( e.g. spring constant same ) only increased
> my simulation time to 10 ns. My histogram now looks like this :-
>>   hist
> <https://docs.google.com/file/d/0B-U8uULVZjfRcVhLN196TXdxcm8/edit?usp=drive_web>
>> I think the shape of the histograms is OK now, they dont appear rocky and
> broken. I suppose I need proper overlap at present with regards to window
> spacing and all.

That's true.

> Kindly review and suggest.

How does the PMF look?  Is it converged?  What are the error estimates from it? 
  Presumably you're interested in free energy differences, so that's what you 
should start by examining.



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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