[gmx-users] bicelle gromacs MD simulation CG model?
ANINDITA GAYEN
aninditagayen at yahoo.co.in
Fri Jun 13 16:30:28 CEST 2008
if i refine the chaps.itp with opls charges, will it be active?
If not, what can i do then? should i use cholesterol in place of chaps?
if yes, where to do download from ?
--- 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/
> >>>>
> >>>>
> >> _______________________________________________
> >>
> >>>>> gmx-users mailing list
> >>>>>
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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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