[gmx-users] to neutralize the system

[Alexander Alexander]

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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