Thanks. If I got your point correctly, then how should I know the end states of the surface-binding process in advance before doing any simulation? And if I start the pre-simulation(just to find the end states) with one of the methods of neutralization, then this affects surely on end states! Regards, Alex
On Wed, Jun 15, 2016 at 12:28 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > So you need to choose a topology for the amino acid that is consistent with > the end states of the surface-binding process (whatever that is). This > drives the answer to the question of what methods for neutralization are > feasible. > > Mark > > On Wed, Jun 15, 2016 at 12:06 PM Alexander Alexander < > alexanderwie...@gmail.com> wrote: > > > Hello, > > > > The final goal is to model the adsorption behavior of a heptapeptide to a > > metal surface, and meanwhile, calculation of the single amino > acid(involved > > in the peptide) binding free energy into the same surface. > > Some of the residues of amino acid are charged, however, their charge > would > > get cancel out (sometime) each other when they come together in the > > heptapeptide. > > > > Thanks, > > Regards, > > Alex > > > > On Wed, Jun 15, 2016 at 11:47 AM, Mark Abraham <mark.j.abra...@gmail.com > > > > wrote: > > > > > 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. > > > > > -- > > 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? 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