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

[bipin singh]

Thanks for your valuable suggestions. I am totally agree with your views.

On Fri, Apr 6, 2012 at 00:11, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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>> 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>
>>    <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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
-----------------------
*Regards,*
Bipin Singh
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