[gmx-users] Counter ion and PME

David Mobley dmobley at gmail.com
Fri Mar 23 17:14:02 CET 2007


> I have read in CSC Course Material that it is possible
> to do not add counter ions in a charged system with
> PME electrostatics , because gromacs (3.3.1 ?) adds a
> background uniform charge to neutralize the system.
> Is this neutralization correct and used in literature?

I can't say much about GROMACS' particular PME implementation here.
But generally this is what PME is supposed to do for a charged system,
since it's impossible to do the sum  if the system is charged -- it
introduces a uniform neutralizing background charge.

Is it "correct"? Well, depends on what you mean by correct. Formally,
the sum works out OK. And since the charge is uniform, it won't affect
the dynamics/thermodynamics. Of course, in real life there is no such
thing as a uniform background charge, and neutralization comes from
counterions. So in that sense it's incorrect.

David Mobley

> Thanks for your help,
> Carlo Camilloni
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