[gmx-users] Non-neutral system

[Ali Alizadeh]

Dear Carsten,

I studied your interesting article. The maximum of positive charge in my
simulation box is about +40e and interface of CO2 with water. The cations
can be

located at the interface. I have a question, if I choose the explicit
uniform background charge approach, can it make sense?

I can not figure out this in your article, for selecting approach we should
perform free energy calculation for each approach. Am I right?

Besides, how can I correct the solvation energy for my periodic system?


On Wed, Apr 23, 2014 at 4:03 PM, Ali Alizadeh <ali.alizadehmojarad at gmail.com
> wrote:

> Dear Carsten,
> Thank you very much for your reply.
> Yes, it is distributed inhomogeneously. In fact I want to investigate the
> solvation energy of cations in water(12 cations, total charge +24e).
> Initial configuration includes cations near the surface of water and then
> they should diffuse into the water bulk.
> Besides, I am reproducing the results of an article(NVT ensemble, Nose
> hoover), so I want to use Ewald for making sure that all options are
> similar. You meant it can be possible with Ewald?
>
> ------------------------------
>
> Hi,
>
> technically, you can use PME with charged systems in Gromacs. However,
> if the charges in your system are distributed inhomogeneously (as, e.g.
> in a water/membrane system), you will get artefacts, as described in
> http://www.mpibpc.mpg.de/14063977/Hub_2014_JCTC.pdf
>
> Best,
>   Carsten
>
>
> On 23 Apr 2014, at 12:58, Ali Alizadeh <ali.alizadehmojarad at gmail.com <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>> wrote:
>
> >* Dear All users,
> *
> > >* I want to simulate a non-neutral system including cations with gromacs. It
> *>* can be possible?
> *> >* I want to use Ewald summation for long for calculating range range
> *>* interactions.
> *> >* I see in Error page of gromacs:
> *> >* Note for PME users: It is possible to use a uniform neutralizing
> *>* background charge in PME to compensate for a system with a net
> *>* background charge. There is probably nothing wrong with this in
> *>* principle, because the uniform charge will not perturb the dynamics.
> *> >* ----------------
> *> >* It means I can not use Ewlad for charged systems?
> *> >* Besides, I can not realize that how neutralization can be done by
> *>* uniform neutralizing background charge. Which part of gromacs do it?
> *> > >* --
> *>* Sincerely
> *> >* Ali Alizadeh*
>
>
> --
> Sincerely
>
> Ali Alizadeh
>



-- 
Sincerely

Ali Alizadeh