Re: [AMBER-Developers] Occasional failures in pmemd serial

From: Jason Swails <>
Date: Thu, 14 Mar 2013 20:21:53 -0400

On Thu, Mar 14, 2013 at 6:17 PM, <> wrote:

> Hello,
> Following the developers' meeting and the emergence of the "domdec" branch
> of pmemd, I'm looking at the state of the CPU code and trying to clear up
> some things as we work to make that one competitive against its
> counterparts in Gromacs and now CHARMM. In order to ensure that what I do
> is sane, I'm running the test suite on pmemd and I notice, out of dozens
> of tests, a few FAILURE warnings.

The Langevin integrator was broken. It looks like you had added a few
things while testing/comparing with mdgx? The commit where it was
introduced is here: 572cc0e695c42d4f39325e883ed17a621544307c

Note that you also committed some changes to sff.c which adds what appears
to be a debug printout. Was this inadvertently added as well? I'm
guessing it should be reversed as well? And the changes to the
test program. My guess is that you did a "git commit -a" or something and
didn't notice the pmemd and sff/nab files in the list of modified files.

I've reversed the changes to dynamics.dat and pmemd tests now pass in

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Thu Mar 14 2013 - 17:30:03 PDT
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