Re: CGMD ? Hydrophobic scale

From: Peter Freddolino (
Date: Fri May 01 2009 - 22:18:00 CDT

Hi Bin,
you may wish to look at the primary reference for the rbcg model in vmd
(Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten.
Journal of Physical Chemistry B, 110:3674-3684, 2006. ) and, more
importantly, the Marrink references cited therein, which describe how
the parameters were derived. This seemed like a better idea to us than
ignoring hydrophobicity.

BIN ZHANG wrote:
> Dear all:
> I was wondering during the development of the amino acid parameters for
> CGMD (Residue Based Coarse Graining Model), has the hydrophobic scale or
> membrane solvation free energy been taken into account? If so, can
> anyone point me a reference for this?
> Thanks a lot.
> Bin

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