[gmx-users] Different results from identical tpr after MD

bipin singh bipinelmat at gmail.com
Thu Apr 5 20:08:20 CEST 2012

Thanks for the reply.
* *I read the link. So, how one can predict something reliable using these
results(based on 50ns in my case) which changes on different machines?
which depends more on the environment of the computer architecture and
other variables of mdrun rather than system (Protein/DNA/RNA) itself for a
short simulation, where we don't have enough resources to run infinitely
long simulation.
And also how to believe the statement made by several research papers based
on unconverged simulations.

On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> bipin singh wrote:
>> Hi all,
>> I am really surprised to see different results from two identical md
>> simulation. I have used identical tpr files for the mdrun (for 50ns) and
>> after the completion of the md job I found that the results from the
>> identical runs is totally different.
>> To further confirm this, I have converted both the input tpr to mdp using
>> gmxdump and diff the two files and found that the mdp is identical.
>> Please let me know what can be the reason of this behaviour. I know that
>> it is unexpected and even I can't believe how can it be possible.
> It is not unexpected at all.  Please consult:
> http://www.gromacs.org/**Documentation/Terminology/**Reproducibility<http://www.gromacs.org/Documentation/Terminology/Reproducibility>
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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Bipin Singh
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