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

[Justin A. Lemkul]

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 <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at 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 <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu> <mailto: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://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

========================================