AMBER Archive (2007)

Subject: Re: AMBER: cutoff & speed-up of GBSA

From: David A. Case (case_at_scripps.edu)
Date: Thu May 31 2007 - 15:31:42 CDT

On Thu, May 31, 2007, Wei Chen wrote:
>
>
> In order to speed up, I have to make cutoff and rgbmax as small as possible.
> >From my single point calculation, I see that a 16 Angstrom cutoff should be
> good. But I am not sure whether I have to use a large value for rgbmax,
> since there is a difference of 500 kcal/mol between rgbmax=16 and
> rgbmax=999, which is 1% of total elec. energy. Using large rgbmax really
> slows down the simulation.

Changing rgbmax changes the physical approximations made in gb theory: the
effects of long-distance atoms on the local effective radii are ignored.
You can't tell whether this is good or bad just by looking at the total
energy. What is important is the way in which the potential energy surface is
changed. And I don't think much is really know about this aspect.

...dac

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