AMBER Archive (2003)

Subject: Re: AMBER: AMBER quasih question(s)

From: David Case (case_at_scripps.edu)
Date: Thu Oct 02 2003 - 06:34:18 CDT

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:      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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu