[gmx-users] Histogram result in free energy calculation

[Justin Lemkul]

On 7/16/15 3:02 AM, minky son wrote:
> Dear GROMACS users.
>
>
>
> I have been studying free energy calculation in Justin tutorial.
>
>
>
> But, I got a somewhat different histogram result compared to the result in
> Justin tutorial.
>
>
>
> I uploaded my result files at the following link:
> http://bio.gnu.ac.kr/~chip/
>
>

The website doesn't load.

>
> I don't know why the result is different.
>
>

Note that the histograms I provide in the tutorial are parsed from the raw (and 
very convoluted) output that gmx bar gives.  You would have to do the same 
separation of data sets to produce those plots, otherwise they will look wildly 
different.  Also note that you shouldn't expect to reproduce the plots exactly 
(like any simulation, there is randomness) but the final free energy values 
should be very robust and absolutely reproducible (I've repeated it several 
times, across multiple GROMACS versions).

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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