Re: What is the atoms limit for Amber 7?

From: David Case <>
Date: Wed 27 Mar 2002 15:45:44 -0800

On Wed, Mar 27, 2002, William Wei wrote:
> Could anybody tell me what is the atom limit under Amber 7 (after solvated)
> while we do minimization or dynamics? In amber 6, I think it is 99999. Thank
> you very much.

Amber 7 *should* work up to 1 million atoms, but that would be so slow as
to not make much sense. We have test cases (see, e.g.
benchmarks/rt_polymerase) that are about 150,000 atoms. I don't know
that anybody has practical experience with systems that are much larger
than this.

Note that to even get close to 1 million atoms, you would need a machine
with a fair amount of memory: for example, the pair list alone for a
periodic system with 500,000 atoms would consume 600 Mbytes of memory.

...hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Mar 27 2002 - 15:45:44 PST
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