[gmx-users] bicelle gromacs MD simulation CG model?
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 13 13:20:50 CEST 2008
ANINDITA GAYEN wrote:
> I have build the itp file from PRODG2 DUNDEE server. and then replaced the stom types from OPLS. Can you comment about the itp file, i can serve that to u.
>
>
Please make sure you are replying to the gmx-users listserv; that way
this thread will be archived for others to benefit from in the future.
I don't think your approach is very sound. The PRODRG server generates
GROMOS-compatible topologies, so supplying OPLS atom types with GROMOS
bond, angle, etc. parameters probably will not lead to a very
self-consistent topology.
As a general note, be aware that the charges and charge groups assigned
by PRODRG are often unsatisfactory, and require refinement.
-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
>> Cc: "Gromacs Users' List" <gmx-users at gromacs.org>
>> Date: Friday, 13 June, 2008, 4:25 PM
>> 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
>>
>>>> ========================================
>>>>
>>>>
>>> Unlimited freedom, unlimited storage. Get it
>>>
>> now, on
>> http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
>>
>>>
>>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>>
>
>
> Meet people who discuss and share your passions. Go to http://in.promos.yahoo.com/groups/bestofyahoo/
>
>
>
--
========================================
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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