[gmx-users] protein-membrane simulation- number of lipids

[Justin Lemkul]

On 10/6/12 1:23 PM, Shima Arasteh wrote:
>
>
>   I want to simulate a system of protein and POPC. I downloaded popc.pdb file from Dr.Klauda website. This pdb file contains 72 lipids. I want to know if this number of lipids would be enough for protein-membrane simukation?
>

Only if it's a very small protein.  Small lipid patches often have problems with 
violations of the minimum image convention if the protein is anything larger 
than a very small peptide, and even then it's questionable.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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