Re: [AMBER] Help with PB simulations using MPI

From: Ray Luo <>
Date: Thu, 18 May 2017 14:11:25 -0700


As the error message says clearly, PBSA does not work with MPI. We
have just removed the last bit of MPI support for PBSA in Amber 2017
and are in the process of immigrating most of PBSA numerical intensive
functions to GPUs instead.

All the best,
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Thu, May 18, 2017 at 12:34 PM, Jake <> wrote:
> Hello,
> I am trying to simulate a small 20 residue all atom peptide in implicit
> solvent with a salt concentration of 150mM (saltcon=0.15). I have performed
> these simulations using Generalized Born model and GBSA without any
> problems in sander.MPI. I am now trying to use the same model with
> Poisson-Boltzmann numerical calculations instead to improve my accuracy
> (igb=10), but I get the following error message:
> "PBSA currently doesn't work with MPI inside SANDER"
> In my script I do not specify anything about surface area calculations. The
> simulation works if I run non MPI sander, but it is significantly slower
> and I will not be able to complete my simulations.
> Is there any way around this bug? Can I use GBSA or some approximation for
> the surface area terms and PB numerical calculations for the electrostatics?
> Thanks.
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Received on Thu May 18 2017 - 14:30:03 PDT
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