Fw: Re: [gmx-users] bicelle gromacs MD simulation CG model?

[ANINDITA GAYEN]

--- On Fri, 13/6/08, ANINDITA GAYEN <aninditagayen at yahoo.co.in> wrote:

> From: ANINDITA GAYEN <aninditagayen at yahoo.co.in>
> Subject: Re: [gmx-users] bicelle gromacs MD simulation CG model?
> To: jalemkul at vt.edu
> 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
> <jalemkul at vt.edu> wrote:
> 
> > From: Justin A. Lemkul <jalemkul at vt.edu>
> > Subject: Re: [gmx-users] bicelle gromacs MD simulation
> CG model?
> > To: aninditagayen at yahoo.co.in, "Discussion list
> for GROMACS users" <gmx-users at 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
> > <aninditagayen at yahoo.co.in> wrote:
> > >
> > >   
> > >> From: ANINDITA GAYEN
> > <aninditagayen at yahoo.co.in>
> > >> Subject: 
> > >> To: gmx-users at 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
> <Mark.Abraham at anu.edu.au>
> > >> Subject: Re: [gmx-users] bicelle gromacs MD
> > simulation CG
> > >> model?
> > >> To: Discussion list for GROMACS users
> > >> <gmx-users at gromacs.org>
> > >> Message-ID:
> <48514D1C.4080108 at anu.edu.au>
> > >> 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/
> > >
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> > >   
> > 
> > -- 
> > ========================================
> > 
> > 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
> > 
> > ========================================
> 
> 
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