[gmx-users] NVIDIA CUDA Alanine Scanning

Szilárd Páll pall.szilard at gmail.com
Tue Aug 7 15:04:31 CEST 2018


Yes, you can use CUDA acceleration, and FEP does work, try to keep
feature-parity between the GPU-accelerated and non-accelerated modes of
GROMACS. Can't comment in depth about GMXPBSA, they may not have full
support for newer releases from what a brief look at their mailing list
Regarding FEP, the caveat is that not all tasks can be offloaded to the
GPU, the free energy short-range computation itself as well as the entire
PME computation has to run on the CPU, and therefore such runs may not
perform on some hardware as efficiently as it would without FEP. That is
especially true if you have very few CPU cores per GPU.

However note that the GROMACS CPU code is rather well tuned so the using
the CPU for some (or all) is not cripplingly slow as you might have seen
with other codes.


On Thu, Jul 26, 2018 at 5:28 PM Matthew Kenney <
matthew.kenney at cellsignal.com> wrote:

> Hi everyone,
> I am attempting to find a means to perform Alanine scanning mutagenesis
> with CUDA acceleration, but have yet to find a free/open-source option.
> AMBER and Schrödinger appear to be the only options available for these
> calculations on CUDA, and I'd like to avoid the hefty industry licences for
> these programs. Hopefully, GROMACS is the solution.
> Does anyone know if the tool GMXPBSA, or Free Energy Perturbation (FEP)
> calculations happen to support CUDA? I ask because many programs I've
> looked at claim overall CUDA support (ex: NAMD/VMD) but do not support FEP
> and certain other types of calculations on CUDA. Any help is much
> appreciated. Thanks!
> Best,
> Matt
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