Re: [gmx-developers] Re: Segmentation fault switching from group to verlet cutoff shceme hess at
Sun Mar 17 18:48:42 CET 2013


I didn't mean to say "drop" when I said low priority.
Changing GPU kernels is nearly trivial and much easier than changing optimized CPU kernels. The main work for most special types of interactions is passing the parameters. If you can live with just two variable parameters, like LJ, for your Buckingham application, implementing this is very easy.



----- Reply message -----
From: "David van der Spoel" <spoel at>
To: "Discussion list for GROMACS development" <gmx-developers at>
Subject: [gmx-developers] Re: Segmentation fault switching from group	to verlet cutoff shceme
Date: Sun, Mar 17, 2013 17:33

On 2013-03-17 17:08, Bu wrote:
> David van der Spoel wrote
>> On 2013-03-16 23:24, Bu Wang wrote:
>>> Hi Berk,
>>> It might be rare in biological simulations, but for simulations of
>>> inorganic materials, it is very common. I think it is a shame that the
>>> scope of GROMACS is limited to biomaterials. Lots of researches in my
>>> field could benefit from the GROMACS' efficiency and functionality. And
>>> some small improvements would enable that.
>>> Anyway, I guess we will have to invest some effort to figure this out
>>> ourselves. To help us get started, do we need cuda programing
>>> experiences to modify this part of the code?
>> How about support for tables on GPU?
> That would be great. We do use other non-bonded potential forms. But I hope
> you are not suggesting that Buckingham as a standard non-bonded potential
> will be dropped in the future versions of GROMACS. If user defined potential
> can be supported, adding Buckingham as a standard potential would not be a
> big hassle, right?
No, rather the diversity will be increased. However I know nothing about 
GPU programming and for me this has low priority, now anyway, although 
this may change if multicore chips and GPUs become more commonplace.

In particular I am interested in the Buckingham variant in this paper as it does not have the 
singularity at short distance.

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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
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