[gmx-users] to neutralize the system

[Alexander Alexander]

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.abraham at 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 <
> alexanderwien2k at 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 <ggroenh at 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 <qasimpars at gmail.com>
> > > To: gmx-users at gromacs.org
> > > Subject: [gmx-users] to neutralize the system
> > > Message-ID:
> > >         <
> > > CAGQgkdSgAweitZmGxMj10p7HcVAzAdqnTc7evJOzPXhmyhmo5A at 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
> > >
> > >
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