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 <[EMAIL PROTECTED]> wrote:
From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] bicelle gromacs MD simulation CG model?
To: [EMAIL PROTECTED], "Discussion list for GROMACS users"
<gmx-users@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
<[EMAIL PROTECTED]> wrote:
From: ANINDITA GAYEN
<[EMAIL PROTECTED]>
Subject:
To: gmx-users@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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] bicelle gromacs MD
simulation CG
model?
To: Discussion list for GROMACS users
<gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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.
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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
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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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