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

[bipin singh]

Yes you are right, that we need to do multiple MD runs before making any
conclusion based on single trajectory. But I have not found any single
research paper which discuss about conclusions drawn based on ensemble of
trajectories. If you have any such research article then please send me the
link.

On Thu, Apr 5, 2012 at 23:50, Peter C. Lai <pcl at uab.edu> wrote:

> Well you're really supposed to conduct multiple runs anyway.
> Remember, a single MD run over a period of time only samples 1 possible
> trajectory out of the ensemble of possible trajectories...
>
> On 2012-04-05 11:38:20PM +0530, bipin singh wrote:
> > 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
> > > MILES-IGERT Trainee
> > > 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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> >
> >
> > --
> > -----------------------
> > *Regards,*
> > Bipin Singh
>
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> ==================================================================
> Peter C. Lai                    | University of Alabama-Birmingham
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-- 
-----------------------
*Thanks and Regards,*
Bipin Singh
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