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

[Mark Abraham]

On 6/04/2012 3:53 PM, bipin singh wrote:
> 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.

Doubtless there are others, but Tsjerk's 
http://dx.doi.org/10.1021/jp068580v is a good start.

Mark

>
> On Thu, Apr 5, 2012 at 23:50, Peter C. Lai <pcl at uab.edu 
> <mailto: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
>     <mailto: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 <http://vt.edu> | (540) 231-9080
>     > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>     <http://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
>     Programmer/Analyst              | KAUL 752A
>     Genetics, Div. of Research      | 705 South 20th Street
>     pcl at uab.edu <mailto:pcl at uab.edu>                     | Birmingham
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> -- 
> -----------------------
> /Thanks and Regards,/
> Bipin Singh
>
>
>

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