Hi Justin,
Can you give me your definition of converged MD and unconverged MD?
Cheers,
Acoot
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Friday, 6 April 2012 4:41 AM
Subject: Re: [gmx-users] Different results from identical tpr after MD
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.
No one can do anything for an infinite amount of time ;) Hence replicate
simulations and thorough statistical analysis are required to obtain reliable
results and prove that what you've done is to be trusted. The other comments
in this thread are quite good so I won't recapitulate other points that have
been made.
> And also how to believe the statement made by several research papers based
> on unconverged simulations.
>
I wouldn't trust any conclusions drawn from demonstrably unconverged
simulations. Not everything that's published has been done correctly. Peer
review is an imperfect system, so be careful what you read and apply good
scientific judgment.
-Justin
> On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul <jalem...@vt.edu
> <mailto:jalem...@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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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> -- -----------------------
> /Regards,/
> Bipin Singh
>
-- ========================================
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
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