Hello Mani,
Membrane-bound protein simulations are still fairly experimental. Usually our membrane-bound protein simulations involve a minimization, careful heating, followed by production.
Definitely take a look at the literature for this: there's already been a good deal of lipid bilayer simulations and the related system parameters. Membrane-bound protein simulations are still fairly cutting-edge, but there's some papers already published.
In particular, the bilayer biophysical parameters are challenging to get correct. What type of bilayer are you using? There are a variety of methods to verify the structural properties of the bilayer, i.e. area per lipid, electron density profile, and others. Can you provide more details about your system?
Ben Madej
Walker Molecular Dynamics Lab
On Jan 14, 2013, at 20:38 PM, Manikanthan Bhavaraju <manikanthanbhavaraju.gmail.com>
wrote:
> I am using Amber12 to simulate membrane-protein system with a
> combination of ff12SB and Lipid11 forcefields. I have modeled the
> system using VMD and converted the files into amber's format. Now, I
> am searching for a procedure to simulate the system. I have read Amber
> Lipid force field tutorial. But I am not quite sure whether the
> procedure given in the tutorial is applicable to a membrane-protein
> system. Is there any generalized procedure suggested by the Amber
> developers? I found 2-3 procedures in the literature for
> membrane-protein simulations. I am not sure which one to choose. Any
> help is really appreciated.
>
>
>
>
> mani
>
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Received on Tue Jan 15 2013 - 09:30:02 PST
