Subject: Re: CCL:Linear scaling algorithms for QM calculations

From: David Gallagher <[email-masked]>
Date: Fri, 01 Mar 2002 07:00:09 -0800

One recent publication suggests that the frontier orbitals on the hydrated 
enzyme (calculated by MOPAC 2000) correlate to the active sites. See:

Effects of Hydration on the Electronic Structure of an Enzyme: Implication 
for Catalytic Function,  Kazuki Ohno et al, J. Am. Chem. Soc. 2001, 123, 
8161-8162

A MOPAC 2002 SCF on Crambin (641 atom protein) takes less than 3 minutes on 
a 1,000 MHz Windows PC and uses only 60 MB of memory.

MOPAC 2002 with the MOZYME linear scaling algorithm handles up to 20,000 
atoms,  for full geometry optimizations and reaction coordinates, and 
includes the COSMO solvent field. The algorithm also scales 
approximately  linearly in memory usage. MOPAC 2002 is available 
stand-alone or as part of CAChe software suite. As the method is fairly 
new, there are not many publications on it's application to proteins around 
just yet. However, there is more information at www.cachesoftware.com

David Gallagher, Fujitsu

At 01:36 AM 3/1/2002 +0100, Julien MICHEL wrote:
>Dear CCLers,
>
>I  recently read a few words about algorithms for pure quantum mechanical
>calculations that scales linearly with the number of electrons in the system
>studied.
>I was surprised to read this as I thought such rate was not feasible for any
>kind
>of quantum calculation. I would be curious to read more about these
>algorithms and how they work. Furthermore, I'd like to know if these
>algorithms have been used to study fairly big molecular systems such as
>proteins. I would be glad if someone could point some references or even
>better internet resources focusing on that topic
>
>Julien MICHEL