[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 <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?
>>
>>
>>
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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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