[gmx-users] GPU

Ehud Schreiber schreib at cgen.com
Tue Jun 12 14:49:26 CEST 2012

>Message: 4
>Date: Mon, 11 Jun 2012 15:54:39 +1000
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] GPU
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4FD5881F.3040509 at anu.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>On 11/06/2012 2:32 AM, ifat shub wrote:
>> Hi,
>> If I understand correctly, currently the Gromacs GPU acceleration does
>> not support energy minimization. Is this so? Are there any plans to
>> include it in the 4.6 version or in a later one (i.e. to allow, say,
>> integrator = steep or cg in mdrun-gpu)? I would find such options
>> extremely useful.

>EM is normally so quick that it's not worth putting much effort into 
>accelerating it, compared to the CPU-months that are spent doing 
>subsequent MD.

Currently, my main use of Gromacs entails running multiple minimizations on an ensemble of states.
Moreover, these states are not obtained using molecular dynamics but rather using the Concoord algorithm.
Therefore, for me the bottleneck is not md but rather minimizations (specifically, cg) and so their acceleration on GPUs would be very advantageous.
If such usage is not totally idiosyncratic, I hope the development team would reconsider GPU accelerating also minimizations.
I suspect this would not be technically too complex given the work already done on dynamics.

Ehud Schreiber.

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