[gmx-users] switching and shifting in GMX 4.6 on GPUs
jesorensen at ucsd.edu
Thu Jan 24 23:20:09 CET 2013
I am running membrane simulations using both the CHARMM36 and MARTINI v. 2.1 parameters.
So both those cut-off treatments are important to me, but if there are ways around it I'd be happy to explore them to be able to use the GPUs. The place it would be most effective would probably be for the all-atom simulations, as the number of particles is much higher in general, so switching would be the most important at this stage.
On a similar note the switching done in gromacs is by the energy - correct? This has been mentioned as an issue for the CHARMM36 lipid parameters as it is the forces that are "normally" switched off in both CHARMM and NAMD, although both options are available there. The difference I am told results in a smaller area/lipid for the bilayers.
On Jan 24, 2013, at 1:09 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> I am not a fan of especially switching the potential, as that produces artifacts.
> Shifting is less harmful, but unnecessary in nearly all cases.
> But I do realize some force fields require this (although you can probably find a cut-off
> setting at which results would be very similar).
> Another reason for not implementing everything right away, is that it would increase the number
> of CPU and GPU kernels by a factor 3.
> What type(s) of LJ cut-off treatments would you consider most important?
> I know that CHARMM uses a switch function and Martini uses shift.
>> From: jesorensen at ucsd.edu
>> Date: Thu, 24 Jan 2013 12:43:30 -0800
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] switching and shifting in GMX 4.6 on GPUs
>> Dear GMX developers,
>> Thanks so much for the GMX 4.6 release. Testing on GPUs has shown impressive speed-ups.
>> I have a question however, regarding the missing "switching and shifting" for non-bonded interactions.
>> I looked at the developer zone website and saw this comment below:
>> * Features currently not supported by the new GPU and SSE kernels:
>> ** Switch and shift interactions (but those are not important, as there is an exact cut-off)
>> While the statement maybe true that they are not "important", some force fields are very particular about the use of switching and shifting, as it is integral to the FF development.
>> So to my question, is there a timeframe for these features being implemented?
>> I realized things like this take time, so I am merely asking out of curiosity.
>> Best regards,
>> gmx-users mailing list gmx-users at gromacs.org
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