<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">The following manuscript may be of interest.<div><br></div><div><a href="http://arxiv.org/abs/math/0610124v2">http://arxiv.org/abs/math/0610124v2</a></div><div><br></div><div>-Robert McGibbon</div><div><br><div><div>On Apr 5, 2012, at 11:26 AM, Acoot Brett wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>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.</span></div><div><span></span>&nbsp;</div><div><span>I am looking forward to getting more feedback on this topic.</span></div><div><span></span>&nbsp;</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> Peter C.
 Lai &lt;<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>&gt;<br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users &lt;<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt; <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, 6 April 2012 4:20 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>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>&gt; Thanks for the reply.<br>&gt; * *I read the link. So, how one can predict something reliable using these<br>&gt; results(based on 50ns in my case) which changes on different machines?<br>&gt; which depends more on the environment of the computer architecture and<br>&gt; other variables of mdrun rather than system
 (Protein/DNA/RNA) itself for a<br>&gt; short simulation, where we don't have enough resources to run infinitely<br>&gt; long simulation.<br>&gt; And also how to believe the statement made by several research papers based<br>&gt; on unconverged simulations.<br>&gt; <br>&gt; On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt; wrote:<br>&gt; <br>&gt; &gt;<br>&gt; &gt;<br>&gt; &gt; bipin singh wrote:<br>&gt; &gt;<br>&gt; &gt;&gt; Hi all,<br>&gt; &gt;&gt;<br>&gt; &gt;&gt; I am really surprised to see different results from two identical md<br>&gt; &gt;&gt; simulation. I have used identical tpr files for the mdrun (for 50ns) and<br>&gt; &gt;&gt; after the completion of the md job I found that the results from the<br>&gt; &gt;&gt; identical runs is totally different.<br>&gt; &gt;&gt;<br>&gt; &gt;&gt; To further confirm this, I have converted both the input tpr to mdp
 using<br>&gt; &gt;&gt; gmxdump and diff the two files and found that the mdp is identical.<br>&gt; &gt;&gt;<br>&gt; &gt;&gt; Please let me know what can be the reason of this behaviour. I know that<br>&gt; &gt;&gt; it is unexpected and even I can't believe how can it be possible.<br>&gt; &gt;&gt;<br>&gt; &gt;&gt;<br>&gt; &gt; It is not unexpected at all.&nbsp; Please consult:<br>&gt; &gt;<br>&gt; &gt; <a href="http://www.gromacs.org/**Documentation/Terminology/**Reproducibility" target="_blank">http://www.gromacs.org/**Documentation/Terminology/**Reproducibility</a>&lt;<a href="http://www.gromacs.org/Documentation/Terminology/Reproducibility" target="_blank">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a>&gt;<br>&gt; &gt;<br>&gt; &gt; -Justin<br>&gt; &gt;<br>&gt; &gt; --<br>&gt; &gt; ==============================**==========<br>&gt; &gt;<br>&gt; &gt; Justin A. Lemkul<br>&gt; &gt; Ph.D. Candidate<br>&gt; &gt; ICTAS Doctoral
 Scholar<br>&gt; &gt; MILES-IGERT Trainee<br>&gt; &gt; Department of Biochemistry<br>&gt; &gt; Virginia Tech<br>&gt; &gt; Blacksburg, VA<br>&gt; &gt; jalemkul[at]vt.edu | (540) 231-9080<br>&gt; &gt; <a href="http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin</a>&lt;<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>&gt;<br>&gt; &gt;<br>&gt; &gt; ==============================**==========<br>&gt; &gt; --<br>&gt; &gt; gmx-users mailing list&nbsp; &nbsp; <a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>&gt; &gt; <a href="http://lists.gromacs.org/**mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/**mailman/listinfo/gmx-users</a>&lt;<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>&gt;<br>&gt; &gt; Please search the archive at <a href="http://www.gromacs.org/**" target="_blank">http://www.gromacs.org/**</a><br>&gt; &gt; Support/Mailing_Lists/Search&lt;<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>&gt;before posting!<br>&gt; &gt; Please don't post (un)subscribe requests to the list. Use the www<br>&gt; &gt; 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>&gt; &gt; Can't post? Read <a href="http://www.gromacs.org/**Support/Mailing_Lists" target="_blank">http://www.gromacs.org/**Support/Mailing_Lists</a>&lt;<a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a>&gt;<br>&gt; &gt;<br>&gt; <br>&gt; <br>&gt;
 <br>&gt; -- <br>&gt; -----------------------<br>&gt; *Regards,*<br>&gt; Bipin Singh<br><br>&gt; -- <br>&gt; gmx-users mailing list&nbsp; &nbsp; <a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>&gt; <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>&gt; 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>&gt; Please don't post (un)subscribe requests to the list. Use the <br>&gt; 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>&gt; 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>Peter C. Lai&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; | University of Alabama-Birmingham<br>Programmer/Analyst&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; | KAUL 752A<br>Genetics, Div. of Research&nbsp;&nbsp;&nbsp; | 705 South 20th Street<br><a href="mailto:pcl@uab.edu" ymailto="mailto:pcl@uab.edu">pcl@uab.edu</a>&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; | Birmingham AL 35294-4461<br>(205) 690-0808&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; |<br>==================================================================<br><br>-- <br>gmx-users mailing list&nbsp; &nbsp; <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></div>-- <br>gmx-users mailing list &nbsp;&nbsp;&nbsp;<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></div></body></html>