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

[Justin A. Lemkul]

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?



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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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