Hi, Sure. But who has data that shows that e.g. a free-energy calculation with the defaults produces lower quality observables than you get with the defaults?
Mark On Wed, Jul 12, 2017 at 5:59 PM Téletchéa Stéphane < stephane.teletc...@univ-nantes.fr> wrote: > Le 11/07/2017 à 15:24, Mark Abraham a écrit : > > Guessing wildly, the cost of your simulation is probably at least double > > what the defaults would give, and for that cost, I'd want to know why. > > Estimated colleague, > > Since this is a wild guess, I'd think to add some guesses myself. I > remember "some time" back having used a lower tolerance on Ewald for > amber simulations (around amber 4/5/6 ...) and it was more common at > this time I presume. This may also be linked to the fact that amber has > a short cut-off at 8 angstrom for electrostatics ... > Someone apparently "ill" at the time already found this stane in 2009: > > > http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/vTjpMdwU/gromacs-preformance-versus-amber > > Out of my memroy, I remembered using 10-6 for Ewald tolerance in AMBER, > and this is mentioned here: > > http://ambermd.org/Questions/ewald.html > > ... apparently linked to DNA simulation as found in JACS 117,4193 (1995) > > In short, this value may come in back and forth for "historical" reasons > (and misuse, of course). > > Others may have additional comments :-) > > Best, > > Stéphane > > > -- > Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein > Design In Silico > UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 > Nantes cedex 03, France > Tél : +33 251 125 636 / Fax : +33 251 125 632 > http://www.ufip.univ-nantes.fr/ - http://www.steletch.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.