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 пишет: > > 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 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. -- 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.
