AMBER Archive (2004)

Subject: Re: AMBER: sander8 performance

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 01 2004 - 14:22:29 CDT


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.

>
> I would like to use sander instead of pmemd because I want to compare
> results from MM-PBSA with those from TI calculations - TI is not
> possible with pmemd, right?

This is correct.

...good luck...dac

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu 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 | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu