On 6/19/16 11:03 AM, Alexander Alexander wrote:
Hello Mark,
I still need help choosing the right method of neutralization of my system.
I am wondering how the final states of the surface-binding process can shed
light on choosing the feasible method of neutralization, here, either
protonation
an rely on
> > the
> > > > > uniform background charge that the PME method introduces if your
> > system
> > > > is
> > > > > charged. The background charge introduces artefacts for
> > non-h
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-h
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.
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
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
> >
act 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
>
Hi Qasim,
Not only should you neutralize the system, but you should add additional
ions too. The behaviour of charged side chains which can find a partner ion
from solution is different from those that can't. You won't see any
problems, but the results will be affected. Not coming across any
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
