[gmx-users] Different Results with Different Platforms

[Mark Abraham]

Hi,

On Tue, Oct 4, 2016 at 4:17 PM Kelechi Okoroafor <kvokoroa at g.syr.edu> 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.
>

It doesn't follow that because you have observed it in under 200ns that it
will always happen in that time, or even that that is a characteristic
time. You have to observe the process quite a few times before you can
express such times with statistical confidence :-) (In isolation, that the
sun was up for about 12 hours today doesn't tell me much about how long
tomorrow will be...) Experiment is not necessarily oracular, either...
there can be other things going on that don't show up with the method being
used there.

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

Of course one cannot rule out that there is a meaningful problem with the
code such that your run(s) with 5.0.6 and 5.1.2 are affected by a bug
(which could even be because 5.0.6 had a bug that was fixed in 5.1.2...).
You should check out the online release notes to see if there's things of
concern for you. But so far, I'd suggest that your problem is merely
insufficient sampling. A physically reasonable result requires that you
have observed reality correctly in an experiment, have used a model capable
of reproducing that reality, have described the system correctly within
that model, have used software that correctly samples according to that
description, and have done enough sampling. Life can be tricky, here :-)

Mark


> --
> Best wishes,
> Kelechi
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