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modeller is not running parallel. The only way to take advantage of
multiple processors is to run parallel modeller jobs. It is useful if
you need to calculate many models for a protein, let say, with various
alignments, or with various templates. Running multiple modeller jobs is
particularly useful if you do loop modeling, since you need to generate
numerous models before you select the one with the lowest energy.
Pay attention that in this case you need to change the RAND_SEED, which
is responsible for random number generation, otherwise you get identical

best  wishes,


------ Forwarded Message
From: Douglas Kojetin <>
Date: Sun, 05 May 2002 23:13:47 -0400
Subject: using modeller w/ multiple CPUs


Does anyone know if MODELLER can take advantage of a multiple CPU
system?  If so, how to set it up?

Many thanks,
Doug Kojetin

Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras