AMBER Archive (2004)

Subject: Re: AMBER: Comparison of simulation results on amber7 and amber 8

From: Sergio E. Wong (swon9_at_itsa.ucsf.edu)
Date: Wed Oct 06 2004 - 11:54:44 CDT

Dear sirs, I was under the impression the CUT parameter in amber7 did
both, cut-off nonbonded interactions AND set a radius for the born radii
calculations. Therefore, the RGBMAX was not infinite; not all of the
atoms were included in the born radii calculations. Am I mistaken?

Thanks

-Sergio

On Wed, 6 Oct 2004, Carlos Simmerling wrote:

> results from the GB model in AMBER 7 and 8 should match, I've done that
> test myself. Make sure that you look at the new variable RGBMAX, it wasn't
> in AMBER7 and can affect the comparison. In AMBER7, the RGBMAX was
> effectively infinite. Otherwise the results will be completely
> comparable, at least
> for IGB=1.
>
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