Re: AMBER: performance with implicit solvent

From: David A. Case <>
Date: Fri, 15 Jun 2007 13:18:31 -0700

On Sat, Jun 16, 2007, Kijeong Kwac wrote:

> Total # of atoms: 32566 (implicit), 151720 (explicit)
> # of steps per hour: 708 (implicit), 4889 (explicit)
> I am wondering why the implicit solvent method take much more time than with
> the explicit water.
> Is this situation normal? Or, could there be something wrong?

This is normal. GB is slow for large systems, whereas, with explicit solvent,
you get the advantage (through PME) of only haveing to use small direct space

As a result, most of the practical work using GB in Amber is for systems an
order of magnitude smaller than what you are looking at.


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Received on Sun Jun 17 2007 - 06:07:37 PDT
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