Hi Richard, Thanks for the reply. It was very helpful. I've looked at the updated manual regarding the x-modifiers and that cleared it up for me.
Best regards, Jesper On Apr 13, 2013, at 4:48 AM, "Broadbent, Richard" <richard.broadben...@imperial.ac.uk> wrote: > > > On 12/04/2013 21:50, "Jesper Sørensen" <jesoren...@ucsd.edu> wrote: > >> Hi Berk and others, >> >> Sorry it has been a long time since this issue was posted, but I got >> side-tracked from this issue with other projects. And I want to make sure >> I understand this correctly before venturing into more simulations. So >> this gets a little long winded, but I hope you will help me figure this >> out. >> >> So following up on the last emails perhaps the nomenclature is not >> consistent among the programs - which I shoudn't expect it to be either, >> so that is okay. >> I know this is the GMX list, but for clarity I will just describe what >> NAMD does, because it relates to how to run lipids in GMX (particularly >> with the GPU). >> NAMD: >> * When the switching function is on: "a smooth switching function will be >> used to truncate the van der Waals potential energy smoothly at the >> cutoff distance". >> * A new "vdwForceSwitching" method is available as of version 2.7 - which >> applies a force-based switching function to the VDW term - similar I >> guess to how CHARMM does it. >> GMX: >> * The switch nomenclature is similar/identical to that in NAMD, in that >> the potential "energy" is switched off. > > I can't speak for what NAMD does but this is not what it means in gromacs > (or any other MD code I've used). Switched adds a function (which starts > at the rcoulomb-switch/rvdw-switch) that smoothly takes both the Energy > and the Force to 0 at the cut-off radius. It is the cut-off scheme used to > parameterise the force-field I use OPLS-AA and I am certain it was used > for many others. It is not supported by the Verlet-cut-off scheme > >> * The "shift" method in Gromacs is equivalent to the "vdwForceSwitching" >> method in NAMD. > > I doubt it but again I've not used NAMD, shift applies a shift to the > Non-bonded potential over its such that the Energy but not the Force goes > to 0 at the cut-off, this method does work with the Verlet cut-off scheme > and is supported on GPU's. If it is not the method used to parameterise > your forcefield, you will have to either perform simulations to check the > effect this has on your system and alter your cut-off's accordingly, or > find a paper that has done this for you in the literature. > >> >> And from what Berk was saying earlier and I heard this from Prof. Lindahl >> during the GPU webinar the other day too, the "shift" method is the only >> appropriate option and switching should not be used. It seems that this >> option is the one used for lipids in NAMD and CHARMM also, so that is >> great. >> >> Now regarding the GPU's you have to run with Verlet groups and here is >> where it get confusing because looking at the comparison table on the >> website "http://www.gromacs.org/Documentation/Cut-off_schemes" ( I've >> extracted the important features of this table below). >> The switched interactions are not available using the Verlet groups and >> that is okay since that shouldn't be used anyways. But, the shifted >> interactions are "available", but only for the "energy" - now did we not >> just agree that when it is the energy that it should be called a >> "switched interaction"? Am I missing something here? > > This is an issue due to you miss understanding the places where these > terms are documented very clearly. > >> >> Non-bonded interaction feature group Verlet >> exact cut-off shift/switch >> X >> cut-off X >> X >> shifted interactions force+energy energy >> switched interactions X >> >> When I asked Prof. Lindahl during the excellent GPU webinar the other >> day, he said that switching was implemented and that is sort of what this >> table says too, but when we try to run a simulation using either switch >> or shift on the GPU we get the following error: >> "With Verlet lists only cut-off LJ interactions are supported" >> >> Now I can switch to an exact cut-off method at the cost of making the >> potential abruptly change to zero at the cut-off - minimizing the >> abruptness can be achieved by extending the cut-off, but then for the >> lipids CHARMM, MARTINI, and others, the cut-off seems to be an integral >> part of the force field development and changing it could prove >> problematic. So this leaves me to think that lipids simulations shouldn't >> be run on the GPU as it is currently, at least not without extensive >> testing. > > In the 4.6 manual and in the online documentation it explains about new > options which are used to control the cut-off scheme see: > http://manual.gromacs.org/online/mdp_opt.html#el > > Using these you can use a shifted cut-off and if necessary for your > Force-field correct for the mild discontinuity in the force either by > looking in the literature or as Berk Hess described below combined with > some test simulations. > > I hope this helps clarify things, > > Richard > >> >> I'd appreciate any comments to all this rambling that can help clarify >> this for me... >> >> Thanks, >> Jesper >> >> >> >> >> >> On Jan 25, 2013, at 12:29 AM, Berk Hess <g...@hotmail.com> wrote: >> >>> >>> 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 >> >> -- >> 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