[gmx-users] Different results from identical tpr after MD
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Apr 6 07:58:01 CEST 2012
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
> AL 35294-4461
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>
> --
> -----------------------
> /Thanks and Regards,/
> Bipin Singh
>
>
>
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