Thank you guys. Johanns, I think one must add counter-ions by himself (which I do not want), as written here http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge
Best regards On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes < j.herm...@lrz.tu-muenchen.de> wrote: > Hey Joao, > > are you sure? I think PME will introduce a neutralizing background charge? > > All the best > > Johannes > > > > On 06.11.2017 11:57, João Henriques wrote: > >> Hi, >> >> You shouldn't use PME without neutralizing the system's charge. It's a >> limitation of the Ewald summation. Take a look at the literature for >> further details. >> >> I don't know much about viscosity, so I'll leave that for someone else. >> >> Cheers, >> J >> >> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh <fpoosa...@gmail.com> >> wrote: >> >> Hi, >>> >>> I have a system containing similar charged atoms. So the total charge is >>> not zero. >>> >>> Simulation results with cut-off coulomb seems reasonable, but using PME >>> they are wrong (total columb potential is negative value which must be >>> positive). Any idea why? >>> >>> If I use counter-ions to neutralize the system, I am afraid the >>> properties >>> I am looking for (viscosity) will be influenced. >>> >>> Best regards >>> -- >>> 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. >>> >>> > -- > ______________________________________ > *Technische Universität München* > *Johannes Hermann, M.Sc.* > Lehrstuhl für Bioverfahrenstechnik > Boltzmannstr. 15 > D-85748 Garching > Tel: +49 8928915730 > Fax: +49 8928915714 > > Email: j.herm...@lrz.tum.de > http://www.biovt.mw.tum.de/ > > > -- > 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.
