<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi Justin,<br><br>Sorry for the mistake, I wrote 0.1 ns in <br><span style="font-weight: bold;">"still there are more fluctuations but and it decreses again to 0.28 nm at 0.1 ns."</span><br>it is 1 ns instead, I ran the simulation for 1ns.<br><br>I have put the job to run for 1 more ns, so may be there I could analyse something as u said.<br>Thanks a lot.<br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Thu, 1/7/10, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] protein stability as a dimer<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Thursday, 1 July, 2010, 5:17 PM<br><br><div class="plainMail"><br><br>sonali dhindwal
wrote:<br>> Hello All,<br>> I have done simulation for 1ns on a protein dimer using GROMOS96 43a1 force field.<br>> I want to study if the protein is stable as a dimer or not, so can you please give me some suggestion as to what analysis I could do for the same.<br>> I checked g_rms after the simulation, graph which I am getting is like, first rmsd is increases rapidly to 0.2nm for for 0.1 ns and<br>> then till 0.8 ns it still increased to 0.3 nm and<br>> still there are more fluctuations but and it decreses again to 0.28 nm at 0.1 ns.<br>> <br>> So what could i infer about the stability of the protein as a dimer from this data.<br><br>If you've only done 100 ps of simulation, not much. I would also question why you consider it a "decrease" from 0.3 nm to 0.28 nm rather than just a fluctuation. Run a longer simulation to gather meaningful RMSD values.<br><br>As for other analysis to do, do some homework in
the literature, and also consider your own goals for running the simulation. Certainly you have a purpose.<br><br>-Justin<br><br>> Thanks in advance.<br>> Regards<br>> <br>> --<br>> Sonali Dhindwal<br>> <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>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=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/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote></td></tr></table><br>