AMBER Archive (2004)

Subject: Re: AMBER: Dielectric Constant

From: David A. Case (case_at_scripps.edu)
Date: Sat Dec 04 2004 - 17:15:10 CST

On Sat, Dec 04, 2004, Marsita M wrote:
>
> I have a confusion regarding the dielectric constant....

No "vacuum" simulation of a protein is likely to yield consistently good
results, at least by the standards one expects today. Without knowing what
sort of calculation you envision, or what you plan to do with the results,
it is impossible to give much good advice. We generally recommend periodic
boundary (PME) simulations with explicit solvent, or generalized Born
simulations, using implicit solvent. But the best way to learn to is to
experiment some yourself: try things and see what happens.

....good luck....dac

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