<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Here I want to talk on the time length of production MD.</span></div><div><span></span> </div><div><span>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.</span></div><div><span></span> </div><div><span>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.</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> Matthew Zwier <mczwier@gmail.com><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 4:24 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>That's an interesting philosophical question.<br><br>In this case, you'll wind up with a 50 ns trajectory where each<br>configuration is consistent with the thermodynamic ensemble you're<br>approximating. That's as close a definition to "realistic" as I
think<br>is worth worrying about. You'd only need to worry about mdrun not<br>giving you exactly reproducible trajectories to 7 or 8 significant<br>figures of precision in atomic coordinates if, simultaneously, nature<br>behaved completely deterministically, you could observe a molecular<br>system with that degree of precision, and your forcefield was exact;<br>none of those three things are true.<br><br>That said, 50 ns seems like a very short time to simulate a complex<br>system like protein/DNA/RNA. I'd be very worried about drawing<br>anything other than observations from such a small data set (because<br>you're almost certainly not converged in your sampling, as you allude<br>to in your final question).<br><br>MZ<br><br>On Thu, Apr 5, 2012 at 2:08 PM, bipin singh <<a href="mailto:bipinelmat@gmail.com" ymailto="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>> wrote:<br>> Thanks for the reply.<br>> I read the link.
So, how one can predict something reliable using these<br>> results(based on 50ns in my case) which changes on different machines?<br>> which depends more on the environment of the computer architecture and other<br>> variables of mdrun rather than system (Protein/DNA/RNA) itself for a short<br>> simulation, where we don't have enough resources to run infinitely long<br>> 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 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 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>>> <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>>><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 | (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>>><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>>> <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>
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>>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>><br>><br>><br>> --<br>> -----------------------<br>> Regards,<br>> Bipin Singh<br>><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>> <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> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www 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>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><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><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 <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<br>www 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>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br> </div> </div> </div></body></html>