[gmx-users] to neutralize the system

[Mark Abraham]

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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