[gmx-users] Gromacs on GPU

[Justin Lemkul]

On 6/16/17 1:55 PM, Mohsen Ramezanpour wrote:
> Dear Gromacs users,
> 
> I would like to use *Gromacs on GPU on supercomputers*. On my desktop, I am
> running on GPU by default. I use the same .mdp parameters and usual Gromacs
> commands which I use for CPUs. Everything looks fine to the best of my
> knowledge.
> 
> I was reading a presentation by Dr. Lindahl on using Gromacs on GPU which
> makes me worried a bit.
> 
> http://on-demand.gputechconf.com/gtc/2013/webinar/gromacs-kepler-gpus-gtc-express-webinar.pdf
> 
> 
> I want to use the charmm36 FF in Gromacs version 5-1-4 for my project.
> I would prefer to keep the parameters as the recommended parameters for
> using Charmm36 in Gromacs package.
> 
> 1) I was wondering if there is any special change required to be made in
> .mdp file?
> 

No.

> 2) Is that necessary to do all the steps (EM, NVT, ...) with GPU or I can
> simply equilibrate my system on my Desktop (say CPU) and then use GPU for
> just the production run?
> 

You do not have to do everything on the GPU.  You can do any or all parts of 
your protocol (though I've never tried EM on a GPU).

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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