Re: [gmx-users] bicelle gromacs MD simulation CG model?

Justin A. Lemkul Fri, 13 Jun 2008 07:44:18 -0700


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 forcefield, and bonded parameters from another. Besides, OPLS is all-atom(although an old UA version exists, too, but I believe it is somewhatold). 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, butgiven the fact that CHAPS has a zwitterionic headgroup, and cholesteroldoes not, I would expect them to behave differently in a bilayer or bicelle.

Either find a paper that details the parameterization of cholesterol foryour desired force field, or derive the parameters for yourself (adifficult task). You can use PRODRG to draw the molecule and get anall-atom .pdb file.


-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]
Cc: "Gromacs Users' List" <gmx-users@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 waythis thread will be archived for others to benefit from in

the future.

I don't think your approach is very sound.  The PRODRG

server generatesGROMOS-compatible topologies, so supplying OPLS atom typeswith GROMOSbond, angle, etc. parameters probably will not lead to averyself-consistent topology.

As a general note, be aware that the charges and charge

groups assignedby PRODRG are often unsatisfactory, and require refinement.


-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]
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 deriveare with are consistent with the original force

field.  It

won't beeasy; the structure of CHAPS has some odd

functional groups

to dealwith, so I don't know that the existing Berger

lipid

parameters will beapplicable, but that doesn't mean they

couldn't be

extended to includeyour molecule. As for a CG model, there are also

some

challenges there,as well. There is a CG topology for cholesterol

online,

which couldserve as a starting framework for CHAPS, but

applying the

appropriateparticles to the rest of the molecule (quaternary

amine,

sulfate) wouldrequire 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 witha 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 ofpertinent 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?



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Virginia Tech
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Justin A. Lemkul
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Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080

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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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