Re: [AMBER-Developers] Fwd: Any similar problem in your mbar output files?

From: Ray Luo <>
Date: Wed, 21 Oct 2020 11:02:46 -0700

Hi Dave,

Indeed, Amber 18 pmemd.MPI has some issues in MBAR energies ... I'll
upload Edward's testing summaries on gitlab.

All the best,
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
---------- Forwarded message ---------
From: Edward King <>
Date: Tue, Oct 20, 2020 at 4:13 AM
Subject: Re: Any similar problem in your mbar output files?
To: Ray Luo <>
AMBER18 pmemd.MPI has mismatching energies, attached are screenshots.
The files are in /home/edward/mbar_cpu
On Tue, Oct 20, 2020 at 10:37 AM David A Case <> wrote:
> On Tue, Oct 20, 2020, Ray Luo wrote:
> >
> >My student did a thorough analysis and found RMSE is 0 kcal/mol if you
> >look at the right places.
> Ray and Edward: thanks.  But it looks(?) like you were testing pmemd.cuda,
> whereas it now appears that the problem may be seen only on the CPU
> version, pmemd.MPI.  Any chance you could run at least one calculation
> using pmemd.MPI?
> Check out  Probably
> easiest to post any results you find there.
> ....regards...dac
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Received on Wed Oct 21 2020 - 11:30:02 PDT
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