AMBER Archive (2004)

Subject: Re: AMBER: sander8 performance

From: Oliver Hucke (ohucke_at_u.washington.edu)
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...

Oliver

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: ohucke_at_u.washington.edu
_______________________________________________________________

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