RE: AMBER: meaningful tax for sander question

From: Cordova, Luis E. <>
Date: Tue, 31 May 2005 16:03:59 -0400

I saw the ABC benchmark reports for the sequence GACT that are in the
range from days to weeks.

Are the input files available for this sequence?


Many thanks,





From: [] On Behalf
Of Cordova, Luis E.
Sent: Tuesday, May 31, 2005 3:20 PM
Subject: AMBER: meaningful tax for sander question




I am trying to benchmark/tax an experimental processor running Amber8,
in particular the sander link.

Does anyone know/could point me to other meaningful examples or
benchmarks that tax the sander link significantly?

Some example that is reported on the literature with results and can be
extended in size and also studied in regards to its scalability varying
for instance the number of processors. One example coming with the
source code of Amber is /benchmarks/dhfr but it takes only seconds to
run on a single processor and there is no documentation for how to make
it bigger or how to extend it or if it is meaningful to the
biochemistry/&c. community.

The problem has to tax the processor preferably while going through the
Ewald and FFT parts of the sander link.

I am particularly interested in problems which demands resources or time
beyond realistic computational constraints.


Many thanks, and I will post back the responses I get,



The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue May 31 2005 - 21:53:00 PDT
Custom Search