Re: AMBER: machine dependent?

From: David A. Case <>
Date: Mon, 11 Aug 2003 13:46:14 -0700

On Mon, Aug 11, 2003, Shuang Ding wrote:
> I'm running a MD simulation of 11mer DNA covalently modified by a carcinogen
> in Amber7. I get a 2.5ns trajectory on our machine OCTANE which has 2 250
> MHZ IP30 Processors and R10000 Chip CPU. But when I use the same protocol to
> run this DNA on our machine ORIGIN 300 with 8 600MHZ IP35 Processors and
> R1400 Chip CPU, the simulation stops with SHAKE error at around 500ps. And
> many repeated runs on both machines show much greater stability on the
> OCTANE, with SHAKE errors much less frequent. Is MD simulation dependent on
> different types of machine?

You should (almost) never get shake failures (on any machine) if you have
vlimit set (please check that). See if the repeated shake failures have to
do with atoms in your covalent may be you are getting strong
forces there (from occasional close contacts). What time step are you using?
Also, it's not clear how many processors you were actually using for these


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 Mon Aug 11 2003 - 21:53:01 PDT
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