I see what you mean now. I thought the peptide was actually moving across the bilayer.
I'd take a close look at the parameters you're using for phospholipids. It's very difficult to get partial charges right for phospholipids. There's a good amount of work and literature available about parameterization of glycerophospholipids for bilayer simulations. It'd be necessary to validate your parameters with a pure bilayer system and take a look at the bilayer biophysical properties to verify that your parameters are reasonable.
Ben Madej
Walker Molecular Dynamics Lab
On Jan 15, 2013, at 10:10 AM, manikanthan bhavaraju <mhb75.msstate.edu> wrote:
> Sure, I will read that paper. The systems consists of 256 POPC
> molecules, 13 cholesterol molecules, and the protein (355 residues + 2
> Ca+2 ions). The POPC bilayer has a cylindrical hole (radius = 12 ang)
> in the center. Using VMD, I have manually inserted the protein into
> the cylindrical hole i.e. 1-20 residues and rest of the protein is
> above the bilayer. Then, I have manually added the cholesterol
> molecules and then solvated the system. The protein has -10 charge so
> I have added 10 Na+ ions. The total size of the system is 100*100*140.
> Further, I am maintaining 0.15M KCl concentration (127 K+, 127 Cl-
> ions) for the entire system. I am interested to analyze the
> interactions between the protein's 1-20 residue with the bilayer. In
> my case, the protein is just bound to the membrane not does not cross.
>
> mani
>
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Received on Tue Jan 15 2013 - 11:00:04 PST
