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

[Justin A. Lemkul]

ANINDITA GAYEN wrote:
> 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?
>
>   

Conceivably, you could do either, as long as the parameters you derive 
are with are consistent with the original force field.  It won't be 
easy; the structure of CHAPS has some odd functional groups to deal 
with, so I don't know that the existing Berger lipid parameters will be 
applicable, but that doesn't mean they couldn't be extended to include 
your molecule.  As for a CG model, there are also some challenges there, 
as well.  There is a CG topology for cholesterol online, which could 
serve as a starting framework for CHAPS, but applying the appropriate 
particles to the rest of the molecule (quaternary amine, sulfate) would 
require thorough evaluation of the atom types available in MARTINI.

-Justin

> --- 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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>   

-- 
========================================

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

========================================