Hi Justin, I have a system of 500 Argon fluid each given a charge +0.20 (vdW cut-off=0.8 nm). So I expect the system to have total positive coulomb potential (repulsion). Below are simualtion results of PME and cut-off:
PME coulomb results: Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- LJ (SR) -2217.86 0.34 24.5444 -0.214063 (kJ/mol) Coulomb (SR) 993.008 0.14 5.39276 -0.435068 (kJ/mol) Coul. recip. -11192.7 0.15 9.86392 -0.470106 (kJ/mol) Potential -12417.5 0.6 33.2669 -1.11921 (kJ/mol) Kinetic En. 1224.39 0.44 44.2301 -2.79584 (kJ/mol) Total Energy -11193.1 0.94 54.8503 -3.91503 (kJ/mol) Conserved En. -17669 710 1446.14 -5008.59 (kJ/mol) Temperature 196.74 0.071 7.10709 -0.449246 (K) Cut-off coulomb results (0.8 nm): Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- LJ (SR) -2231.64 0.58 24.2735 2.05241 (kJ/mol) Coulomb (SR) 94520.2 4.7 221.879 -9.05937 (kJ/mol) Potential 92288.5 4.5 217.531 -7.00686 (kJ/mol) Kinetic En. 1257.31 0.43 45.3804 0.778738 (kJ/mol) Total Energy 93545.9 4.1 221.992 -6.22759 (kJ/mol) Conserved En. 518736 40000 81842.2 283452 (kJ/mol) Temperature 197.031 0.069 7.29193 -0.125132 (K) Best regards On Mon, Nov 6, 2017 at 1:06 PM, João Henriques <joao.m.a.henriq...@gmail.com > wrote: > Hi Johannes, > > I just meant that from a purely theoretical point of view, it needs to be > neutral. This has to do with the convergence of the outer infinite series, > as the paper Micholas linked clearly states. I sincerely hope I'm not > botching this up, but this is the conclusion I've withdrawn from reading > the literature. Now, if the software implementation contains some tricks to > account for this, that I'm not familiar with and will therefore leave that > discussion for someone else more acquainted with it. > > Cheers, > J > > > > 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. > -- 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.