Subject: Re: CCL:New linear scaling method

From: "Victor Anisimov" <[email-masked]>
Date: Wed, 16 Apr 2003 09:11:26 +0200

Dear CCLers,

John McKelvey has asked me a question regarding the local minimum
problem. I believe the problem is very important to be discussed on the
list. Therefore I post my answer to the list.

----- Original Message -----
From: <[email-masked]>

> Victor,
>
> How would the problem of local minima be handled if the program were to do
a
> geometry optimizatopn on 10**5 atoms?
>
> Regards!
>
> John McKelvey

Dear John,

Perhaps you agree, that the local minimum problem is a separate one to
the linear scaling solution of the diagonalization of Fock matrix. LocalSCF
method itself resolves just the diagonalization problem. The same do other
respected linear scaling methods, e.g. MOZYME, D&C, CG-DMS.

However I agree that the local minimum problem has to be addressed if one
is serious about protein modeling. This requires molecular dynamics
averaging
applied after some preliminary structure refinement done by geometry
optimization.

Taking the present program code one can do full geometry optimization
for 100,000+ real protein on a single-CPU PC. I bet QM MD for about
1,000 atoms protein is a feasible job for a 10 CPUs Linux cluster nowadays.
Although this has to be implemented first.

Full QM MD modeling of proteins is not a long future. The present LocalSCF
code
works just on 1 CPU. Being parallelized it could utilize about 1000 CPUs
quite
effectively. This unusual level of parallelization is not just my
imagination.
This capability comes from extremely  high localization level of the
LocalSCF
method. As the LocalSCF preprint shows, LMOs expanded just on 30 atomic
centers are enough to get 0.001 RMS error on atomic charges. This level of
localization is extremely favorable for parallelization.

We already made some tests on 1 CPU machine applying D&C technique on
the top of LALM, which is a similar to the LocalSCF engine. 1,000,000 atoms
irregular linear peptide built from random combination of 14 different amino
acids
was divided on 300 fragments. Calculating each fragment sequentially on the
one CPU gave the energy converged in 7 hours. Of course, the convergence
criterion was quite loose but this was enough to show a feasibility of the
D&C / LocalSCF concept.

I believe the publishing of the LocalSCF paper makes a valuable contribution
for
the wide dissemination of the idea. As I mentioned in my previous posting
the
preprint is available from the Chemistry Preprint Server by URL
http://preprint.chemweb.com/physchem/0304005
The server requires registration, but the registration is free.

Hope, I answered your question.

With kind regards,
Victor

--
Victor Anisimov
FQS Poland

---

From: [email-masked]
Date: Wed, 16 Apr 2003 07:07:14 +0000

Hello,

My comments were in fact related to optimization of geometries for systems
having 10**5 atoms, i.e. very large systems.  This being made feasable because
of  MOPAC's extremely fast LocalSCF procedure.

John McKelvey