[gmx-users] Different Results with Different Platforms

[Justin Lemkul]

On 10/4/16 10:16 AM, Kelechi Okoroafor wrote:
> Thank you very much, Mark, for your prompt response; it is highly appreciated.
> My sincere apologies for the miscommunication in my initial post.
>
> I meant to say that in performing several repetitions of simulations,
> after approximately 200ns of total simulation time on (Stampede and my
> school's) cluster, I observed some structures formed that have been
> corroborated by other MD simulations as well as experiments.
>
> However, these same simulations were repeated several times on both my
> personal desktop computers and I did not observe the expected
> structures after 200ns.
>

This sounds like normal sampling variability.  It's never a given that 
independent simulations will do the same thing in the same amount of time.

> So the issue is not that the simulations are not exactly the same; it
> is that the simulations are not giving physically reasonable results.

Does your desktop implementation of GROMACS pass all tests?  If it does, then 
there's nothing wrong with the results.

-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 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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