Hey, It might also be related to the PBC, with gromacs not writing whole molecules anymore. Maybe a link to a picture would be good, showing protein beads spheres, together with the (triclinic) unit cell.
Cheers, Tsjerk On Mon, Sep 6, 2010 at 12:05 PM, XAvier Periole <[email protected]> wrote: > > Dear Itamar, > If your problem is not a bond length definition in VMD (which > you can overcome by using "dynamic bonds", although it is not > perfect) you may have a problem in your topology. > The way you describe your problem (groups of bids moving freely) > suggests that you do have a topology problem. > XAvier. > On Sep 6, 2010, at 11:52 AM, Itamar Kass wrote: > > Thanks Mark for the replay, > I used VDW presentation to over come it. > Best, > Itamar > > On 6/09/2010 6:33 PM, Mark Abraham wrote: > > ----- Original Message ----- > From: Itamar Kass <[email protected]> > Date: Monday, September 6, 2010 14:06 > Subject: [gmx-users] Protein stability using MARTINI > To: Discussion list for GROMACS users <[email protected]> > >> HI all, >> >> I am simulating a protein in water using the MARTINI (CG) force >> field. My protein composed of few alpha-helices and a big tail >> (~50AA) which is random coiled. I have built the simulation >> system according to the procedure at >> http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in- >> water . >> >> After a 10ns simulation, I have visualised the system using VMD. >> It seems like the protein had dismantled to amino acids. I see >> groups of bids moving freely in the system. > > 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 :-) > > Mark > >> >> Any idea of the problem? Any idea how to fix it? >> >> PS I don't want to use elastic network for the random coil tail, >> as I wish to capture as much conformation as possible. >> >> Thanks in advance, >> Itamar. >> >> -- >> >> >> "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: [email protected] >> ============================================ >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > > > "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: [email protected] > ============================================ > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
