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

[Robert McGibbon]

The following manuscript may be of interest.

http://arxiv.org/abs/math/0610124v2

-Robert McGibbon

On Apr 5, 2012, at 11:26 AM, Acoot Brett wrote:

> But we hope finally no matter which trajectory, a stable protein conformation should be got! As for during the production MD, no significant energy change included.
>  
> I am looking forward to getting more feedback on this topic.
>  
> Acoot
> 
> From: Peter C. Lai <pcl at uab.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
> Sent: Friday, 6 April 2012 4:20 AM
> Subject: Re: [gmx-users] Different results from identical tpr after MD
> 
> 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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