From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jan 15 2009 - 09:24:11 CST
Hi Bin,
this is all explained in the relevant references (Marrink et al., JPCB
108:750-760 for the lipid/water model, Shih et al., JPCB 110:3674-3684
for the first generation of the rbcg model in namd). As explained there,
the dielectric of 20 is one of a couple measures taken to compensate for
the lack of orientable dipoles in, say, water in the CG model. You
really ought to read the papers for the parameterization details.
Best,
Peter
BIN ZHANG wrote:
> Hi all:
>
> Can someone explain to me why usually dielectric is not left as default
> (set to 20) in CGMD (rbcg) ? To get better agreement with All-Atom
> Simulation?
>
> Also, how is the parameter chosen? Is it the same for only water system
> and water lipid system?
>
> Thanks a lot.
>
> Bin
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> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood
> of patriots and tyrants.
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