Subject: Re: CCL:MOPAC2000 and MOLZYME

From: "Victor Anisimov" <[email-masked]>
Date: Fri, 6 Aug 1999 09:36:11 +0200

Deepak Singh wrote:

>Does anyone have experience with the MOLZYME module of MOPAC2000.  We
>have been running it of a DELL XPS-T500 and it requires a LOT of memory
>for minimizing a 28 kDa protein.  Does anyone have a memory requirement
>for something like a SGI Octane?
>

SGI Octane does not bring special memory benefits for MOPAC2000 jobs comparing
with other hardware/software platforms. And the solution is to specify BFGS
keyword.

Single point calculation in MOPAC2000 (MOZYME) requires unbelievably small
memory
even for huge size proteins (5000 atoms - 500Mb) but gradient optimization needs
more
memory. Default optimization method is EF which is very memory consuming one.
Usually it
requires 10-20 times more memory than single point calculation. BFGS is 5 times
less
memory demanding one and usually it is the best for very large molecules in
MOPAC2000
(MOZYME).

Hope, it helps.
Victor.

=========================================================================
Victor Anisimov, PhD, Software Researcher - Computational Chemistry
FQS Poland, Palac Pugetow, ul. Starowislna 13-15, 31-038 Krakow, Poland
Email: [email-masked]  Tel.(+48 12) 429 4345  Fax(+48 12) 429 6124
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