AMBER Archive (2008)

Subject: RE: AMBER: Test failure with Amber 10

From: Ross Walker (
Date: Wed Nov 26 2008 - 10:30:42 CST

Hi Kevin,

> run with the PMEMD implementation of Sander (stated on line 6 of
> which outputs some additional information including
> the fields highlighted in the test difference.

This shouldn't matter. Bob has done a LOT of work on PMEMD to make it fully
compatible with sander and results should be identical although when running
in parallel different summation orders can lead to round off differences.
However a test case run with PMEMD should pass when compared using dacdif
against a test case save file generated with sander and vice versa. Indeed
the tip5p test case passes on my machine with both sander and pmemd so I
think what you are seeing is just your compiler rounding things in a
different way that as Dave says for a very short run can give marked
differences in the RMS.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)