[gmx-users] Using GPU to do simulations

[Szilárd Páll]

On Thu, Apr 17, 2014 at 8:45 PM, <mircial at sjtu.edu.cn> wrote:

> Hi everyone,
>
> I am trying to do some pulling simulations by gromacs (i.e., pull a ligand
> from its binding site), as the system is large I want to accelerate the
> simulations by GPU. I want to confirm that, Does GPU simulation support the
> pulling code of GROMACS? Can I use GPU acceleration to do simulations in
> which a ligand is pulled out of its binding site?
> I am asking this, as I see from the website that the pulling code is not
> supported by GPU (Supported Features Section of
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM#Compiling_and_installation_of_GROMACS-GPU_from_source
> ).
>

As the first section of the page you linked states, the page refers to
GROMACS-OpenMM, the GPU acceleration implementation in v4.5 (based on the
OpenMM library) and starting with 4.6 is (almost completely) replaced by
the native GPU acceleration. The pages relevant to the current
implementation are:
http://www.gromacs.org/Documentation/Cut-off_schemes
http://www.gromacs.org/GPU_acceleration
http://www.gromacs.org/Documentation/Acceleration_and_parallelization

Cheers,
--
Szilárd


> Thanks very much for your help.
>
> With my best regards,
> Ruo-Xu Gu
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