From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] bicelle gromacs MD simulation CG model?
To: [EMAIL PROTECTED]
Cc: "Gromacs Users' List" <gmx-users@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
<[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.
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
========================================
