Hi, Such an answer starts with "what are you trying to model?"
Mark On Wed, Jun 15, 2016 at 11:45 AM Alexander Alexander < alexanderwie...@gmail.com> wrote: > Hello, > > How about neutralization of these cases, a single amino acid (zwitterionic > form) > or a peptide in aqueous solution; > I was wondering which of below methods is preferable for neutralizing the > system? > One is the introducing a counter-ion(Na or Cl for example) and the second > one is the protonation(or deprotonaton) the amino acid or peptide by > adding or removing one Hydrogen atom, so, > > Thanks, > Regards, > Alex > > On Wed, Jun 15, 2016 at 8:47 AM, Groenhof, Gerrit <ggro...@gwdg.de> wrote: > > > You always need to neutralise with counter-ion, rather than rely on the > > uniform background charge that the PME method introduces if your system > is > > charged. The background charge introduces artefacts for non-homogeneous > > systems by placing charge uniformly across the system rather than inside > > the higher dielectric. For further explanation and quantification of the > > artifact see the paper by Hub et al: > > http://pubs.acs.org/doi/abs/10.1021/ct400626b > > > > Gerrit > > > > > > Message: 4 > > Date: Wed, 15 Jun 2016 01:00:40 +0300 > > From: Qasim Pars <qasimp...@gmail.com> > > To: gmx-us...@gromacs.org > > Subject: [gmx-users] to neutralize the system > > Message-ID: > > < > > cagqgkdsgaweitzmgxmj10p7hcvazadqntc7evjozpxhmyhm...@mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Dear gmx users, > > > > I am confused on below questions: > > > > 1) Is it necessary to neutralize a protein without ligand? Does the PME > > method work with a charged protein correctly? > > > > 2) I have done lots of MD simulations at a charged complex structure > > (protein+ligand) with the PME method using GROMACS. I haven't come across > > with any problems because of the charge of the system. It means that the > > PME method works at a charged complex system properly. In spite of that, > do > > you think that I need to neutralize a charged complex system? > > > > Can anyone comment on above questions? > > > > Cheers, > > > > -- > > Qasim Pars > > > > > > ------------------------------ > > > > -- > > 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. > > > > End of gromacs.org_gmx-users Digest, Vol 146, Issue 68 > > ****************************************************** > > -- > > 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.
