Re: AMBER: AMBER quasih question(s)

From: David Case <>
Date: Thu, 2 Oct 2003 04:34:18 -0700

On Mon, Sep 29, 2003, Rachel Ward wrote:

> I'm attempting to run a trajectory for a ~3500 atom protein and some
> structural waters through quasih, and would prefer to run more than 50
> snapshots (default maximum in our version). Are there performance
> issues noted when overriding the default maxima in place (nat=800,
> last=50, nmode=50)? Any comments would be appreciated.

quasih scales reasonably well to larger systems. 3500 atoms should be
slow-ish but doable, even if you want all of the eigenvectors. Memory
will probably be the first limitation you would hit.

.....good luck....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
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu Oct 02 2003 - 12:53:01 PDT
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