AMBER Archive (2004)

Subject: Re: AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 03 2004 - 21:31:06 CDT

On Wed, Jun 02, 2004, xiaowei li wrote:

> I have seen that you mentioned epsilon=4r was necessary for normal
> modes calculation of nucleic acid in several emails. Now I am confused
> epsilon =4r is only for igb=1 case or for all the situations.

There are no second derivatives available (yet) for any of the gb models.
So, if you want to do normal modes, you have to use some compromise. The
model mentioned is one such compromise. I'm not sure what you mean by
the phrase "all the situations".

...dac

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