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

[Acoot Brett]

Here I want to talk on the time length of production MD.
 
I have a professor on computational biology. She said for MD only several ps is enough. I have the expereince to run production MD for several ns, and I have got stable conformation.
 
But I am sure for some protein system, even a 50 ns MS will not give the stable conformation, thus maybe the results are not reproducible. I am not sure whether my explaination is suitable to you.
 
Cheers,
 
Acoot
 

________________________________
 From: Matthew Zwier <mczwier at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, 6 April 2012 4:24 AM
Subject: Re: [gmx-users] Different results from identical tpr after MD
  
That's an interesting philosophical question.

In this case, you'll wind up with a 50 ns trajectory where each
configuration is consistent with the thermodynamic ensemble you're
approximating.  That's as close a definition to "realistic" as I think
is worth worrying about.  You'd only need to worry about mdrun not
giving you exactly reproducible trajectories to 7 or 8 significant
figures of precision in atomic coordinates if, simultaneously, nature
behaved completely deterministically, you could observe a molecular
system with that degree of precision, and your forcefield was exact;
none of those three things are true.

That said, 50 ns seems like a very short time to simulate a complex
system like protein/DNA/RNA.  I'd be very worried about drawing
anything other than observations from such a small data set (because
you're almost certainly not converged in your sampling, as you allude
to in your final question).

MZ

On Thu, Apr 5, 2012 at 2:08 PM, bipin singh <bipinelmat at gmail.com> 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> 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
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> 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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>
>
>
> --
> -----------------------
> Regards,
> Bipin Singh
>
>
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