[gmx-users] Non-neutral system

[Ali Alizadeh]

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