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

[Acoot Brett]

But we hope finally no matter which trajectory, a stable protein conformation should be got! As for during the production MD, no significant energy change included.
 
I am looking forward to getting more feedback on this topic.
 
Acoot
 

________________________________
 From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, 6 April 2012 4:20 AM
Subject: Re: [gmx-users] Different results from identical tpr after MD
  
Well you're really supposed to conduct multiple runs anyway.
Remember, a single MD run over a period of time only samples 1 possible 
trajectory out of the ensemble of possible trajectories...

On 2012-04-05 11:38:20PM +0530, 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.
> 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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==============================**==========
> > --
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> 
> 
> 
> -- 
> -----------------------
> *Regards,*
> Bipin Singh

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