--- On Fri, 13/6/08, ANINDITA GAYEN <[EMAIL PROTECTED]> wrote:
> From: ANINDITA GAYEN <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] bicelle gromacs MD simulation CG model? > To: [EMAIL PROTECTED] > Date: Friday, 13 June, 2008, 4:09 PM > You can find my paper on Langmuir vol 24, Issue 10, pages > 5422-5432 2008, I have made two bicelle samples > experimentally, and now i want to model those two bicelles > theorically to connect the theory with the NMR experimental > data. I have euilibrated a dmpc bilayer in OPLS-BERGER force > field already, but confused about the incorporation of chaps > since it is not a bilayer component. I have 128 lipid square > bilayer. Is it possible to model such a bilayer that will > have chaps at the edge from this force field or may i use > the coarse grain model to build it? can you suggest > anything? > > --- On Fri, 13/6/08, Justin A. Lemkul > <[EMAIL PROTECTED]> wrote: > > > From: Justin A. Lemkul <[EMAIL PROTECTED]> > > Subject: Re: [gmx-users] bicelle gromacs MD simulation > CG model? > > To: [EMAIL PROTECTED], "Discussion list > for GROMACS users" <gmx-users@gromacs.org> > > Date: Friday, 13 June, 2008, 3:54 PM > > Can you be more specific as to what you need help on? > > I'm familiar with > > a couple of these papers, and the methods sections are > > quite good. > > Files are freely available on S.J. Marrink's site, > as > > well as a list of > > pertinent publications detailing their methodology. > > > > -Justin > > > > ANINDITA GAYEN wrote: > > > > > > --- On Fri, 13/6/08, ANINDITA GAYEN > > <[EMAIL PROTECTED]> wrote: > > > > > > > > >> From: ANINDITA GAYEN > > <[EMAIL PROTECTED]> > > >> Subject: > > >> To: gmx-users@gromacs.org > > >> Date: Friday, 13 June, 2008, 9:56 AM > > >> Hi, > > >> > > >> I several papers of Marrink, Siewert J.; > Mark, > > Alan E, > > >> and in a paper of Yong Jiang, bicelles are > modeled > > with CG > > >> model. > > >> > > >> JCP 126, 045105 (2007) Jiang Y. > > >> Biophys. j. 87 182-192 Jiang Y. > > >> Effect of Undulations on Surface Tension in > > Simulated > > >> Bilayers > > >> > > >> Marrink, S. J.; Mark, A. E. J. Phys. Chem. > B.; > > (Article); > > >> 2001; 105(26); 6122-6127. DOI: > 10.1021/jp0103474. > > >> Molecular Dynamics Simulations of Mixed > Micelles > > Modeling > > >> Human Bile > > >> > > >> Marrink, S. J.; Mark, A. E. > > >> Biochemistry; (Article); 2002; 41(17); > 5375-5382. > > >> > > >> Molecular Dynamics Simulation of the > Kinetics of > > >> Spontaneous Micelle Formation > > >> Marrink, S. J.; Tieleman, D. P.; Mark, A. E. > > >> J. Phys. Chem. B.; (Article); 2000; 104(51); > > 12165-12173. > > >> > > >> > > >> Can someone help me? > > >> > > >> > > >> Message: 7 > > >> Date: Fri, 13 Jun 2008 02:21:48 +1000 > > >> From: Mark Abraham > <[EMAIL PROTECTED]> > > >> Subject: Re: [gmx-users] bicelle gromacs MD > > simulation CG > > >> model? > > >> To: Discussion list for GROMACS users > > >> <gmx-users@gromacs.org> > > >> Message-ID: > <[EMAIL PROTECTED]> > > >> Content-Type: text/plain; charset=UTF-8; > > format=flowed > > >> > > >> ANINDITA GAYEN wrote: > > >> > > >>> hi all, > > >>> > > >>> can someone give me information how to > model a > > bicelle > > >>> > > >> using gromacs? I have dmpc:chaps as the > bicelle > > components, > > >> and i came to know that coarse grain model > can > > help me. > > >> > > >>> But, the picture is still not clear. > Please > > help me to > > >>> > > >> make the bicelle in gromacs. > > >> > > >> Have you searched the web and the literature > to > > see if > > >> anybody else has > > >> done something like this? > > >> > > >> > > >> > > >> Bring your gang together. Do your > thing. > > Find your > > >> favourite Yahoo! group at > > >> http://in.promos.yahoo.com/groups/ > > >> > > > > > > > > > Explore your hobbies and interests. Go to > > http://in.promos.yahoo.com/groups/ > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.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 > > > > > > > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Graduate Research Assistant > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > > Unlimited freedom, unlimited storage. Get it now, on > http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/ Explore your hobbies and interests. Go to http://in.promos.yahoo.com/groups/ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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. 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