Acoot Brett wrote:
Hi Justin,
Can you give me your definition of converged MD and unconverged MD?
One could fill many textbook chapters with an answer to this question. Suffice
it to say that one would consider a simulation converged if the properties of
interest have also converged around stable values, such that extending the
simulation longer would not change the result. Knowing when to stop is not
something that can be generalized, and depends entirely upon the system at hand,
question being asked, and method(s) of analysis. Structural, thermodynamic, or
other energetic properties may be of interest, but these are things you should
define before you even sit down at your terminal to begin.
-Justin
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> <mailto: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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--
========================================
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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