AMBER Archive (2004)

Subject: Re: AMBER: A few questions in the protein unfolding simulations using GB model

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 29 2004 - 21:59:24 CST

On Thu, Jan 29, 2004, Jiayun Pang wrote:
>
> I am using Amber7 with the mpi run before. As you suggested, I have a
> shorter run with single processor. The dimer run is 4.2 times longer the
> monomer run. It seems the time allocation among GB parameters are different.

Amber 7 GB is not well optimized for large systems, and (as noted) there
are some parts (particularly the "diag" part) that scale poorly as the
system gets bigger. Things should be considerably better in Amber 8.

..regards...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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