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On 6/04/2012 3:53 PM, bipin singh wrote:
<blockquote
cite="mid:CAKb2Z-Hk6mf0zZgsGH9TceOejmt6TXFjPwkEQHgBSHvUxkS-Gg@mail.gmail.com"
type="cite">Yes you are right, that we need to do multiple MD runs
before making any conclusion based on single trajectory. But I
have not found any single research paper which discuss about
conclusions drawn based on ensemble of trajectories. If you have
any such research article then please send me the link.<br>
</blockquote>
<br>
Doubtless there are others, but Tsjerk's
<a class="moz-txt-link-freetext" href="http://dx.doi.org/10.1021/jp068580v">http://dx.doi.org/10.1021/jp068580v</a> is a good start.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKb2Z-Hk6mf0zZgsGH9TceOejmt6TXFjPwkEQHgBSHvUxkS-Gg@mail.gmail.com"
type="cite">
<br>
<div class="gmail_quote">On Thu, Apr 5, 2012 at 23:50, Peter C.
Lai <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Well you're really supposed to conduct multiple runs anyway.<br>
Remember, a single MD run over a period of time only samples 1
possible<br>
trajectory out of the ensemble of possible trajectories...<br>
<br>
On 2012-04-05 11:38:20PM +0530, bipin singh wrote:<br>
> Thanks for the reply.<br>
> * *I read the link. So, how one can predict something
reliable using these<br>
<div class="im">> results(based on 50ns in my case) which
changes on different machines?<br>
> which depends more on the environment of the computer
architecture and<br>
> other variables of mdrun rather than system
(Protein/DNA/RNA) itself for a<br>
> short simulation, where we don't have enough resources
to run infinitely<br>
> long simulation.<br>
> And also how to believe the statement made by several
research papers based<br>
> on unconverged simulations.<br>
><br>
> On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>
wrote:<br>
><br>
> ><br>
> ><br>
> > bipin singh wrote:<br>
> ><br>
> >> Hi all,<br>
> >><br>
> >> I am really surprised to see different results
from two identical md<br>
> >> simulation. I have used identical tpr files
for the mdrun (for 50ns) and<br>
> >> after the completion of the md job I found
that the results from the<br>
> >> identical runs is totally different.<br>
> >><br>
> >> To further confirm this, I have converted both
the input tpr to mdp using<br>
> >> gmxdump and diff the two files and found that
the mdp is identical.<br>
> >><br>
> >> Please let me know what can be the reason of
this behaviour. I know that<br>
> >> it is unexpected and even I can't believe how
can it be possible.<br>
> >><br>
> >><br>
> > It is not unexpected at all. Please consult:<br>
> ><br>
</div>
> > <a moz-do-not-send="true"
href="http://www.gromacs.org/**Documentation/Terminology/**Reproducibility"
target="_blank">http://www.gromacs.org/**Documentation/Terminology/**Reproducibility</a><<a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Reproducibility"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a>><br>
> ><br>
> > -Justin<br>
> ><br>
> > --<br>
> > ==============================**==========<br>
<div class="im">> ><br>
> > Justin A. Lemkul<br>
> > Ph.D. Candidate<br>
> > ICTAS Doctoral Scholar<br>
> > MILES-IGERT Trainee<br>
> > Department of Biochemistry<br>
> > Virginia Tech<br>
> > Blacksburg, VA<br>
> > jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> | (540)
231-9080<br>
</div>
> > <a moz-do-not-send="true"
href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>**<a
moz-do-not-send="true"
href="http://vt.edu/Pages/Personal/justin" target="_blank">vt.edu/Pages/Personal/justin</a><<a
moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>><br>
> ><br>
> > ==============================**==========<br>
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> --<br>
> -----------------------<br>
> *Regards,*<br>
> Bipin Singh<br>
<div class="im"><br>
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</div>
==================================================================<br>
<span class="HOEnZb"><font color="#888888">Peter C. Lai
| University of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a moz-do-not-send="true" href="mailto:pcl@uab.edu">pcl@uab.edu</a>
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-- <br>
<span style="color:rgb(51,51,255)">-----------------------</span><br
style="color:rgb(51,51,255)">
<i><span style="color:rgb(51,51,255)">Thanks and Regards,</span></i><br
style="color:rgb(51,51,255)">
<span style="color:rgb(51,51,255);font-family:garamond,serif">Bipin
Singh</span><br>
<br>
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