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: jesoren...@ucsd.edu > Date: Thu, 24 Jan 2013 14:20:09 -0800 > To: gmx-users@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 <g...@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: jesoren...@ucsd.edu > >> Date: Thu, 24 Jan 2013 12:43:30 -0800 > >> To: gmx-users@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 > >> > >> > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
