<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Justin,</span></div><div><span></span> </div><div><span>Can you give me your definition of converged MD and unconverged MD?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</span></div><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, 6 April 2012 4:41 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Different results from identical tpr after MD<br> </font> </div> <br><br><br>bipin singh wrote:<br>> Thanks for the reply.<br>> / /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.<br><br>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.<br><br>> And also how to believe the statement made by several research papers based on unconverged simulations.<br>> <br><br>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.<br><br>-Justin<br><br>> On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" ymailto="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<br>> identical md simulation. I have used identical tpr files for the<br>> mdrun (for 50ns) and after the completion of the md job I found<br>> that the results from the identical runs is totally different.<br>> <br>> To further confirm this, I have converted both the input tpr to<br>> mdp using gmxdump and diff the two files and found that the mdp<br>> is identical.<br>> <br>> Please let me know what can be the reason of this behaviour. I<br>> know that it is unexpected and even I can't believe how can it<br>> be possible.<br>> <br>> <br>> It is not unexpected at all. Please consult:<br>>
<br>> <a href="http://www.gromacs.org/__Documentation/Terminology/__Reproducibility" target="_blank">http://www.gromacs.org/__Documentation/Terminology/__Reproducibility</a><br>> <<a 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>> 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]vt.edu <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>> <a
href="http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin</a><br>> <<a 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>> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/__mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/__mailman/listinfo/gmx-users</a><br>> <<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>><br>> Please search the archive at<br>> <a href="http://www.gromacs.org/__Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/__Support/Mailing_Lists/Search</a><br>> <<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www<br>> interface or send it to <a href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a
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