[gmx-users] to neutralize the system

[Groenhof, Gerrit]

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>
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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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