Re: AMBER: sander8 performance

From: David A. Case <case.scripps.edu>
Date: Tue, 1 Jun 2004 12:22:29 -0700

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 

-- 
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David A. Case                     |  e-mail:      case.scripps.edu
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Received on Tue Jun 01 2004 - 20:53:00 PDT
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