[gmx-users] Using GPU to do simulations

[Justin Lemkul]

On 4/17/14, 2:45 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).
>

This page was obsolete years ago when version 4.6 introduced native GPU support. 
  AFAIK the pull code should work.  If it doesn't, mdrun will complain loudly 
and you'll have your answer in seconds!

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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