[gmx-users] Gromacs on GPU

[Mohsen Ramezanpour]

Thanks Justin.

So, can we say that simulation on CPU and GPU (as far as we use the same
version of Gromacs) are compatible?

If yes, is that okay to continue a simulation which was done with CPU (say
till 100 ns) to 500 ns (using GPU)?
Or I should start from t=0 with GPU?

It is important for my case as the allocations on supercomputers change
from CPU to GPU. So, not sure if I should start all again or it is fine to
continue.

Cheers


On Fri, Jun 16, 2017 at 12:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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-ke
>> pler-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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