AMBER Archive (2004)

Subject: Re: AMBER: sander8 performance

From: Oliver Hucke (
Date: Tue Jun 01 2004 - 14:46:06 CDT

So, the "hb" benchmark was done with pmemd?
In the bench.hb script sander seems to be used...


David A. Case wrote:
> On Tue, Jun 01, 2004, Oliver Hucke wrote:
>>With a sytem of ~50000 atoms, PME, cut=8.0, I get 75000 steps per day,
>>using two processors. This seems rather poor compared to the 117000
>>steps that were obtained in the hemoglobin benchmark with two Xeon
>>processors (2.0 GHz), with ifc7 compiled amber8, as I read on the amber
>>benchmarks page.
> This probably mostly reflects the relative efficiency of sander vs. pmemd.


Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: _______________________________________________________________

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