Subject: Linear scaling algorithms for QM calculations

From: "Julien MICHEL" <[email-masked]>
Date: Fri, 1 Mar 2002 01:36:33 +0100

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

---

From: Andrew Horsfield <[email-masked]>
Date: Fri, 1 Mar 2002 13:32:16 +0000 (GMT)

> 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

A good overview of the theory can be found in the review article

 Stefan Goedecker, Reviews of Modern Physics 71, 1085 (1999)

For data on performance for quantum chemistry applications, the papers of
Gustavo Scuseria are useful. For example:

 J. M. Millam and G. E. Scuseria, Journal of Chemical Physics 106, 5569 (1997)
 A. Daniels and G. Scuseria, Journal of Chemical Physics 110, 1321 (1999)
 K. Nemeth and G. Scuseria, Journal of Chemical Physics 113, 6035 (2000)

Cheers,

Andrew

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From: "Dr. Martin Schuetz" <[email-masked]>
Date: Fri, 1 Mar 2002 15:42:03 +0100 (MET)

For coupled cluster methods with linear scaling check references
on my web site

----------------------------------------------------------------------------
PD Dr. Martin Schuetz                         Phone: 0049 (0)711-685-4397
University of Stuttgart                       Fax:   0049 (0)711-685-4442
Institute for Theoretical Chemistry
Pfaffenwaldring 55                            Room Nr: 8.161
D-70569 Stuttgart
Email: [email-masked]
WWW  : http://www.theochem.uni-stuttgart.de/~schuetz/
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On Fri, 1 Mar 2002, Julien MICHEL wrote:

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From: Matt Challacombe <[email-masked]>
Date: Fri, 1 Mar 2002 01:58:02 -0700

Hi Julien,

You can have a look at our web site (www.t12.lanl.gov/~mchalla), which is 
woefully out of date (will bring it to the present soon). It does however 
have some background papers that you may find relevant.  We have a fully O(N) 
code that is getting close to beta quality, which does the following in TRUE 
O(N) for 3-D insulating systems: Orthogonalization, solution of SCF 
equations, exact exchange, exchange-correlation and Coulomb sums.  It does
geometry optimization and PBCs for pure DFT.  

-Matt

On Thursday 28 February 2002 05:36 pm, Julien MICHEL wrote:
> 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
> algorithms and how they work. Furthermore, I?d like to know if these
> [email-masked] -- archive search    |    Gopher: gopher.ccl.net
> 70 Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan:
> [email-masked]

-- 
Matt Challacombe, Ph.D.           http://www.t12.lanl.gov/~mchalla/ 
Los Alamos National Laboratory    email: [email-masked]           
Group T-12, Mail Stop B268        phone: (505) 665-5905           
Los Alamos, New Mexico  87545     fax:   (505) 665-3909

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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:
>algorithms and how they work. Furthermore, I'd like to know if these