[gmx-developers] Re: Segmentation fault switching from group to verlet cutoff shceme

David van der Spoel spoel at xray.bmc.uu.se
Sun Mar 17 17:33:05 CET 2013

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 
http://pubs.acs.org/doi/abs/10.1021/ct300826t 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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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