[gmx-users] Reproducibility in free energy calculations.

[Justin Lemkul]

On 4/19/14, 1:16 AM, sujithkakkat . wrote:
> Hello Justin,
>
>     I tried the free energy calculations in your tutorial at different sets
> of conditions. Also I repeated a simulation at the same conditions with
> same parameters, thrice on the same computer on same number of processors.
> The results in the three cases where different (4.16 +/- 0.19 , 4.36
> +/-0.14 , 4.54 +/-0.15 kJ/mol ) . I am not surprised, since I thought that
> this might happen to a small system (241 water + 1 methane). However, I
> want to be sure that this is OK. I guess in cases like this I should go for
> an average value of many runs.
>

Offhand, I would have expected slightly better agreement between the runs, but 
there are tons of factors at play, so the outcome seems very plausible and 
reasonably consistent.

-Justin

-- 
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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 601
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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