[gmx-users] bicelle gromacs MD simulation CG model?
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 13 16:43:28 CEST 2008
ANINDITA GAYEN wrote:
> if i refine the chaps.itp with opls charges, will it be active?
>
>
I doubt it; you're still using nonbonded parameters from one force
field, and bonded parameters from another. Besides, OPLS is all-atom
(although an old UA version exists, too, but I believe it is somewhat
old). Gromos force fields are UA.
> If not, what can i do then? should i use cholesterol in place of chaps?
> if yes, where to do download from ?
>
If you believe cholesterol will suffice to emulate CHAPS, then yes, but
given the fact that CHAPS has a zwitterionic headgroup, and cholesterol
does not, I would expect them to behave differently in a bilayer or bicelle.
Either find a paper that details the parameterization of cholesterol for
your desired force field, or derive the parameters for yourself (a
difficult task). You can use PRODRG to draw the molecule and get an
all-atom .pdb file.
-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, 4:50 PM
>> 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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>>>>>>>
>>>>>>>
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>>>>
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>>>>
>>>>
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>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
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>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>>>
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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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>
>
>
--
========================================
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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