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

From: David A. Case <>
Date: Thu, 29 Jan 2004 19:59:24 -0800

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.


David A. Case                     |  e-mail:
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            |
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Received on Fri Jan 30 2004 - 18:56:04 PST
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