[gmx-users] switching and shifting in GMX 4.6 on GPUs

[Berk Hess]

Hi,

The nomenclature is confusing here.
I don't recall the details of the switching in CHARMM.
But switch in Gromacs refers to switching the potential.
Shift in Gromacs refers to switching the force and thereby shifting the potential.

A switch on the force only (thus "shift" in Gromacs) can usually be matched pretty
well by a plain cut-off with shifted potential by choosing the cut-off such that either
the LJ potential matches the potential over the non-switched area or the total LJ potential
energy matches for the system of interest. I expect these two cut-offs to be very similar.

Cheers,

Berk

----------------------------------------
> Subject: Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs
> From: jesorensen at ucsd.edu
> Date: Thu, 24 Jan 2013 14:20:09 -0800
> To: gmx-users at gromacs.org
>
> Hi Berk,
>
> 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.
>
> Best,
> Jesper
>
> On Jan 24, 2013, at 1:09 PM, Berk Hess <gmx3 at hotmail.com> wrote:
>
> >
> > Hi,
> >
> > 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.
> >
> > Cheers,
> >
> > Berk
> >
> > ----------------------------------------
> >> 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:
> >>
> >> http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6
> >> * 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,
> >> Jesper
> >>
> >>
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