Re: [AMBER] MacOS pmemd.cuda

From: David Cerutti <>
Date: Thu, 29 Mar 2018 15:54:34 -0400

The -macAccelerate flag is only going to call an optimized blas/lapack
library bundles with its OS. For standard MD simulations blas and lapack
are inconsequential--there are hardly any matrix operations to do. To get
the cuda code you need to do ./configure -cuda clang, then make install.
If you do not have an NVIDIA GPU in your Macintosh, this is all we
currently support. AMD support is a work in progress but there are much
larger edits to the code to finish for the time being.

On Thu, Mar 29, 2018 at 3:21 PM, Kadir Ozcan <>

> Hello,
> My PI has recently purchased Amber16 and I am attempting to run GPU
> accelerated MD using pmemd, as non-GPU pmemd is giving me at most 10 ns/day
> for my simulation. Is it possible to use GPU accelerated pmemd on MacOS
> High Sierra Version 10.13.1 (17B1003)? I have an Intel HD Graphics 630 1536
> MB. I’ve already configured, installed, and tested AmberTools17 as well as
> Amber16 by following the instructions in the manual I was able to
> successfully install GPU accelerated pmemd using “./configure
> -macAccelerate clang", followed by "make install” and “make test”. However
> when I enter “pmemd.cuda” into the terminal, I am told "command not found”.
> Thank you in advance.
> Regards,
> Kadir Ozcan
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Received on Thu Mar 29 2018 - 13:00:02 PDT
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