Thanks a lot to all, for your insights. Right now I am running some simulations in order to study the influence of some settings - my ions seem to aggregate more now than in the previous simulations with Amber, but I will wait for longer simulated time.
I am not skilled enough to study the code itself. I also had a careful look at the manuals. Better, I thought I had a careful look, because I missed the settings that you reported. Thanks again for you help. Best regards, Tmmaso ________________________________________ Da: [email protected] [[email protected]] per conto di Hannes Loeffler [[email protected]] Inviato: giovedì 5 maggio 2016 15.40 A: [email protected] Cc: [email protected] Oggetto: Re: [gmx-users] Suggested settings for using Amber force field in Gromacs On Thu, 5 May 2016 13:20:59 +0000 "Casalini Tommaso" <[email protected]> wrote: > Thanks a lot for your quick answer. > > I am trying to reproduce with Gromacs some results that I obtained > with Amber software. I put the same thermostat (Langevin) and > barostat (Berendsen with isotropic scaling) with same time constant, > the same dt, the same cutoff, and so on. You will have to carefully study the manuals for both packages (read the code actually...), check your settings and see how close you can get. But you will need to accept that differences in implementation for possible lack thereof may exist. How much your particular system will depends on such details, I don't know. BTW, the defaults settings for pmemd/sanders are vdwmeth = 1 (vdW long-range dispersion correction on) and fswitch = -1 (truncation cutoff). Cheers, Hannes. -- 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 [email protected]. -- 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 [email protected].
