Acoot Brett wrote:
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.
Several ps is insufficient for all but the fastest (and thus smallest) motions
in a macromolecule like a protein.
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.
The time frame necessary depends on what you're hoping to see. Fast motions
(like side chain rotation, etc) require short simulations. Domain motions or
folding simulations may require hundreds of ns or even more. Some phenomena
cannot be modeled efficiently by atomistic MD simulations, though other
mesoscale approaches may perform better.
-Justin
Cheers,
Acoot
*From:* Matthew Zwier <mczw...@gmail.com>
*To:* Discussion list for GROMACS users <gmx-users@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 <bipinel...@gmail.com
<mailto:bipinel...@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 <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
>>
>> -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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--
========================================
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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