<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Dear Itamar,<div><br></div><div>If your problem is not a bond length definition in VMD (which</div><div>you can overcome by using "dynamic bonds", although it is not</div><div>perfect) you may have a problem in your topology. </div><div><br></div><div>The way you describe your problem (groups of bids moving freely) </div><div>suggests that you do have a topology problem.</div><div><br></div><div>XAvier. </div><div><br><div><div>On Sep 6, 2010, at 11:52 AM, Itamar Kass wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div bgcolor="#ffffff" text="#000000"> <div bidimailui-direction-uniformity="ltr" dir="ltr" style="direction: ltr;" bidimailui-generated="true">Thanks Mark for the replay, </div> <div bidimailui-direction-uniformity="neutral" bidimailui-generated="true"> </div> <br> <div bidimailui-direction-uniformity="ltr" dir="ltr" style="direction: ltr;" bidimailui-generated="true">I used VDW presentation to over come it. </div> <div bidimailui-direction-uniformity="neutral" bidimailui-generated="true"> </div> <br> <div bidimailui-direction-uniformity="ltr" dir="ltr" style="direction: ltr;" bidimailui-generated="true">Best, </div> <div bidimailui-direction-uniformity="ltr" dir="ltr" style="direction: ltr;" bidimailui-generated="true">Itamar </div> <br> <br> On 6/09/2010 6:33 PM, Mark Abraham wrote: <blockquote cite="mid:fbb28bd8118d5.4c8533dc@anu.edu.au" type="cite"><br> <br> ----- Original Message -----<br> From: Itamar Kass <a class="moz-txt-link-rfc2396E" href="mailto:itamar.kass@monash.edu"><itamar.kass@monash.edu></a><br> Date: Monday, September 6, 2010 14:06<br> Subject: [gmx-users] Protein stability using MARTINI<br> To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br> <br> > HI all,<br> > <br> > I am simulating a protein in water using the MARTINI (CG) force <br> > field. My protein composed of few alpha-helices and a big tail <br> > (~50AA) which is random coiled. I have built the simulation <br> > system according to the procedure at <br> > <a class="moz-txt-link-freetext" href="http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in">http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in</a>-<br> > water .<br> > <br> > After a 10ns simulation, I have visualised the system using VMD. <br> > It seems like the protein had dismantled to amino acids. I see <br> > groups of bids moving freely in the system.<br> <br> I'm not sure what you mean here, but it seems likely that VMD's heuristics for guessing where bonds between atoms might exist aren't going to work well for a coarse-grained protein. There's probably a standard solution, for which you should Google :-)<br> <br> Mark<br> <br> > <br> > Any idea of the problem? Any idea how to fix it?<br> > <br> > PS I don't want to use elastic network for the random coil tail, <br> > as I wish to capture as much conformation as possible.<br> > <br> > Thanks in advance,<br> > Itamar.<br> > <br> > -- <br> > <br> > <br> > "In theory, there is no difference between theory and practice. <br> > But, in practice, there is." - Jan L.A. van de Snepscheut<br> > <br> > ===========================================<br> > | Itamar Kass, Ph.D.<br> > | Postdoctoral Research Fellow<br> > |<br> > | Department of Biochemistry and Molecular Biology<br> > | Building 77 Clayton Campus<br> > | Wellington Road<br> > | Monash University,<br> > | Victoria 3800<br> > | Australia<br> > |<br> > | Tel: +61 3 9902 9376<br> > | Fax: +61 3 9902 9500<br> > | E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a><br> > ============================================<br> > <br> > -- <br> > gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> > <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> > Please search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> <br> > before posting!<br> > Please don't post (un)subscribe requests to the list. Use the <br> > www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br> > Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a> </blockquote> <br> <pre class="moz-signature" cols="72">--
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a>
============================================
</pre> </div> -- <br>gmx-users mailing list <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/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/mailing_lists/users.php</blockquote></div><br></div></body></html>