AMBER Archive (2003)

Subject: AMBER: machine dependent?

From: Shuang Ding (sd517_at_nyu.edu)
Date: Mon Aug 11 2003 - 13:39:10 CDT

Dear Amber Users,

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?
Thanks a lot for your advice.

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