[gmx-users] Self-assembly lipid simulation

[Tsjerk Wassenaar]

Hi Alif,

Probably papers from Alex de Vries and Siewert-Jan Marrink will be
good to start with (mind not to take the coarse-grained ones, unless
that's what you want to do ;)) Also consider that self-assembly is not
really different from bilayer/monolayer simulations.

Best,

Tsjerk

On 8/29/07, Syma Khalid <syma.khalid at bioch.ox.ac.uk> wrote:
>
>
>
>
> Hi,
>
>
>
> The GROMACS user manual is a good place to start. For more specific help you
> will probably need to provide details of exactly what you want to do.
>
> What are you simulating? What are the questions you are hoping to answer?
>
>
>
>
>
> Best wishes,
>
>
>
> -Syma
>
>
>
>
> ********************************************************************
>
>  Dr. Syma Khalid                    e-mail:  syma.khalid at bioch.ox.ac.uk
>  Dept. of Biochemistry              phone:   (0)1865-275380
>  University of Oxford               fax:     (0)1865-275273
>  South Parks Road
>  Oxford
>  OX1 3QU
>  U.K.
>  ________________________________
>
>  ________________________________
>
>
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Alif M Latif
>  Sent: 29 August 2007 19:19
>  To: gmx-users at gromacs.org
>  Subject: [gmx-users] Self-assembly lipid simulation
>
>
>
>
>
> Dear Gromacs users,
>
>
>
>
>
> I'm doing MD Simulation on self-assembly of lipid molecules using gromacs.
> If someone can kindly help me find the conditions (for my .mdp file) for
> these kind of simulation? There are many choices and i would like to ask for
> opinion on general (usually) conditions used in the .mdp file for the
> simulation. I would like to look for physical and some thermodynamical
> properties from my simulation results. This is to aid the experimental
> results done.
>
>
>
>
>
> Any paper or links also can help me a lot. I have read many papers but i
> thought maybe u guys can help add more to it. This is because not much
> options i can find in those papers and not all of them use gromacs.Thanks
> for reading and your help is greatly appreciated. Thanks again.
>
>
>
>
>
> ----------------------------------------------------------------------------------------------------------------------------------
>
>
>
>
>
> M. Alif M. Latif
>
>
> Chemistry Department, Faculty of Science,
>
>
> Universiti Putra Malaysia,
>
>
> 43400 UPM Serdang, Selangor,
>
>
> Malaysia
>
>
>  ________________________________
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623