On Fri, Feb 19, 2016 at 1:23 PM, Timofey Tyugashev <tyugas...@niboch.nsc.ru> wrote:
> And here my hope for quick and easy solution hath end. > All of the points you make ring true. Especially ones about software > engineering and funding in science (or maybe I'm more familiar with them). > > Actually, ne relatively recent paper, "Phosphorylation of PPARγ Affects > the Collective Motions of the PPARγ-RXRα-DNA Complex" ( > http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008), > uses AMBER99SB-ILDN with GROMACS 4.6 and Justin Lemkul is listed as the > first author. And the simulated structure is a protein-DNA complex. So it > should be very close to my case. > The one thing that looks strange to me: both rvdw (LJ interacions) and > box-solute distance set at 1.0 nm. Shouldn't the latter be larger to avoid > probable periodic image interactions problems? > Otherwise, looks like my settings are generally the same, except > forgetting that LINCS allows 2fs step. > I guess you meant 4-5 fs *if* combined with virtual sites. At 2 fs you can use h-bond only constraints if i) you prefer the resulting physics or ii) you want to have a bit better performance and a lot better scalability. > > > 17.02.2016 19:45, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: > >> Message: 4 >> Date: Wed, 17 Feb 2016 13:45:46 +0000 >> From: Mark Abraham<mark.j.abra...@gmail.com> >> To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: Re: [gmx-users] correct rlist and Verlet scheme >> Message-ID: >> < >> camnumarkusmbzbrvneie35aahdwkpo-mgbejewxzgpueew6...@mail.gmail.com> >> Content-Type: text/plain; charset=UTF-8 >> >> >> Hi, >> >> Yes, what you say is true, but very much "in short" and AFAIK true of all >> MD packages.:-) >> >> If e.g. AMBER (or anyone else) has a test suite for any force field, then >> we'll seriously consider implementing it, to e.g. verify before each >> release.:-) IMO, defining such a suite is a research topic itself - >> particularly as the original parameterizations did so in the context of >> limitations in the methods of the day. If a force field was parameterized >> with a fixed buffer because nobody then knew how large a buffer was >> necessary for a given quality of relevant observable, it does not follow >> that the only possible acceptable practice now is to use that fixed >> buffer. >> >> Similar considerations apply to things like e.g. the use of long-ranged >> corrections for dispersion interactions. e.g. AMBER99 was parameterized >> without such corrections, so probably has built into its parameters some >> compensating errors, and any kind of validation-by-replication should in >> principle not use such corrections. But these days, I think that nobody >> would actually recommend parameterizing a force field without something >> like that, and experience suggests that using one is an improvement, even >> if though the change is not officially sanctioned anywhere that I know of. >> IMO showing that some range of force fields shows satisfactory agreement >> with experiment under certain .mdp setting combinations is useful evidence >> of an implementation that is valid, and that is what one can see in the >> literature. >> >> The state of the art in software engineering is that nobody much has time >> to test all the things that they'd like to test. (One large exception is >> software for control of devices that potentially affect human health.) >> Scientific software development has additional challenges because the >> people doing it are often lacking in formal training in best practice, and >> have to appear to publish science, in order to keep attracting funding, >> and >> this directly conflicts with spending time on good software engineering >> practice that granting and tenure committees will ignore later in their >> careers... >> >> Mark >> >> On Wed, Feb 17, 2016 at 1:01 PM Timofey Tyugashev<tyugas...@niboch.nsc.ru >> > >> wrote: >> >> >In short, FFs were tested to some degree when they were added in GROMACS >>> >to reproduce AMBER results, but there is no certainty if they actually >>> >do this now and 'correct' mdp settings to run them are unknown. For any >>> >of the versions that are listed in GROMACS. >>> >Is that correct, or I'm missing something in translation? >>> > >>> >16.02.2016 18:03,gromacs.org_gmx-users-requ...@maillist.sys.kth.se >>> ?????: >>> >>>> > >Message: 2 >>>> > >Date: Tue, 16 Feb 2016 11:23:06 +0000 >>>> > >From: Mark Abraham<mark.j.abra...@gmail.com> >>>> > >To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se >>>> > >Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue >>>> > > 76 >>>> > >Message-ID: >>>> > > < >>>> >>> >camnumasutdhr8sot1qt4xdczogsdjsfgo8umiuhrpffxxfa...@mail.gmail.com> >>> >>>> > >Content-Type: text/plain; charset=UTF-8 >>>> > > >>>> > >Hi, >>>> > > >>>> >>>> > >The ports of all the AMBER force fields were all tested to reproduce >>>> >>> >AMBER >>> >>>> > >when when they were added to GROMACS. Many of our regressiontests use >>>> >>> >those >>> >>>> > >force fields, so there is reason to expect that they all continue to >>>> >>> >work. >>> >>>> > >The Verlet scheme is tested to implement what the documentation says >>>> it >>>> > >does. There have been bugs introduced (and fixed) in how GROMACS >>>> > >preprocessing tools implement the requirements of AMBER force fields, >>>> > >including ILDN. >>>> > > >>>> > >To be able to say "this force field is tested to work correctly with >>>> this >>>> > >cutoff scheme in this version of GROMACS" requires the community to >>>> agree >>>> > >on what that means, e.g. a large collection of single-point >>>> >>> >energies+forces >>> >>>> > >agree to within a certain precision, and simulations done in a >>>> particular >>>> > >model physics produce these ensembles with these observables, etc. >>>> That >>>> > >hasn't happened yet. As far as I know, the ability of the different >>>> AMBER >>>> > >code versions to correctly continue to implement all the AMBER force >>>> >>> >fields >>> >>>> > >has a similar kind of question mark over it. Just having the same >>>> name is >>>> > >not enough;-) >>>> > > >>>> > >Mark >>>> > > >>>> > >On Tue, Feb 16, 2016 at 11:17 AM Timofey Tyugashev< >>>> >>> >tyugas...@niboch.nsc.ru> >>> >>>> > >wrote: >>>> > > >>>> >>>>> > >> >So, are there any other Amber force fields more suitable and more >>>>>> >>>>> >tested >>> >>>> > >> >for GROMACS? >>>>>> > >> > >>>>>> > >> >15.02.2016 21:00, >>>>>> gromacs.org_gmx-users-requ...@maillist.sys.kth.se >>>>>> >>>>> >?????: >>> >>>> > >>> > >Message: 1 >>>>>>>> > >>> > >Date: Mon, 15 Feb 2016 13:15:02 +0000 >>>>>>>> > >>> > >From: Mark Abraham<mark.j.abra...@gmail.com> >>>>>>>> > >>> > >To:gmx-us...@gromacs.org, >>>>>>>> gromacs.org_gmx-users@maillist.sys.kth.se >>>>>>>> > >>> > >Subject: Re: [gmx-users] correct rlist and Verlet scheme >>>>>>>> > >>> > >Message-ID: >>>>>>>> > >>> > > < >>>>>>>> >>>>>>> > >> > >>>>>> camnumatmbmgvbfj49ez+4k_bftdmkyfyiw5iz-eecwicujb...@mail.gmail.com> >>>>>> >>>>>>> > >>> > >Content-Type: text/plain; charset=UTF-8 >>>>>>>> > >>> > > >>>>>>>> > >>> > >Hi, >>>>>>>> > >>> > > >>>>>>>> > >>> > >On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev< >>>>>>>> >>>>>>> > >> >tyugas...@niboch.nsc.ru> >>>>>> >>>>>>> > >>> > >wrote: >>>>>>>> > >>> > > >>>>>>>> >>>>>>>>> > >>>>> > >> >I've studied the relevant sections of the manual, >>>>>>>>>>>> but I don't >>>>>>>>>>>> >>>>>>>>>>> >consider >>> >>>> > >>>>> > >> >myself to be familiar enough with this field to >>>>>>>>>>>> successfully >>>>>>>>>>>> >>>>>>>>>>> >guess the >>> >>>> > >>>>> > >> >right settings. >>>>>>>>>>>> > >>>>> > >> > >>>>>>>>>>>> > >>>>> > >> >ff99sb-ildn is included in the gromacs >>>>>>>>>>>> distribution, so >>>>>>>>>>>> >>>>>>>>>>> >shouldn?t be >>> >>>> > >>>>> > >> >there some recommended settings for it? >>>>>>>>>>>> >>>>>>>>>>> > >>> > >Ideally, yes. But nobody has made a particular effort >>>>>>>> for that >>>>>>>> >>>>>>> > >> >combination. >>>>>> >>>>>>> > >>> > > >>>>>>>> > >>> > >Or else how was it tested to run >>>>>>>> >>>>>>>>> > >>>>> > >> >properly? >>>>>>>>>>>> > >>>>> > >> > >>>>>>>>>>>> >>>>>>>>>>> > >>> > >In principle, one would have to e.g. show that >>>>>>>> > >>> > >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/ >>>>>>>> can be >>>>>>>> >>>>>>> > >> >replicated. >>>>>> >>>>>>> > >>> > >That's not a straightforward proposition... >>>>>>>> >>>>>>> > >> >-- >>>>>> > >> >Gromacs Users mailing list >>>>>> > >> > >>>>>> > >> >* Please search the archive at >>>>>> > >> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >>>>>> before >>>>>> > >> >posting! >>>>>> > >> > >>>>>> > >> >* Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists >>>>>> > >> > >>>>>> > >> >* For (un)subscribe requests visit >>>>>> > >> > >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>> or >>>>>> > >> >send a mailtogmx-users-requ...@gromacs.org. >>>>>> >>>>> > >>> >-- >>> >Gromacs Users mailing list >>> > >>> >* Please search the archive at >>> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> >posting! >>> > >>> >* Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists >>> > >>> >* For (un)subscribe requests visit >>> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> >send a mail togmx-users-requ...@gromacs.org. >>> >> ------------------------------ >> >> -- Gromacs Users mailing list * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. End of >> gromacs.org_gmx-users Digest, Vol 142, Issue 96 >> ****************************************************** >> > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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