AMBER Archive (2007)

Subject: AMBER: interior dielectric constant

From: Miguel Ferreira (tetrass_at_hotmail.com)
Date: Tue Feb 20 2007 - 11:22:31 CST

Hi

I want to run a MD of a mitochondrial protein. I read that the mitochondrial
matrix is the most crowded aqueous cellular compartment, and hence, the
amount of water is much less than that of the cytoplasm. So, to represent
such an environment I am thinking in run an implicit MD with an interior
dielectric constant of 4. Does anyone know if this is correct?

Thanks
Miguel

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