Re: [AMBER] Question about how a charged system can be simulated using PBC?

From: Dr. Vitaly Chaban <>
Date: Sun, 8 Jun 2014 12:27:05 +0200

That is an old story... Counter-charge is implicitly added in some PME
implementations, so formally it is OK to forget about the absence of
the counter-ion.

You need PBC only if you need to control pressure, right? In all other
cases, why not to go a bit non-traditional and simulate a cluster?

Dr. Vitaly V. Chaban

On Sun, Jun 8, 2014 at 6:12 AM,
<> wrote:
> Hello,
> I want to modeling the hydration structure of Na+ using periodic boundary condition.
> I wonder please how to creat my system? A metal ion and hundreds of water molecules (Reported papers did)?
> The charge of my system is +1. If the periodic boundary condition is used, that is,
> there are infinite number of same mirror images distributed in the three dimensional space.
> Then, the electrostatic potential energy will be infinite large, which means that the energy of a unit cell is infinite.
> I think that once the periodic boundary condition is used, the system's charge, dipole moment should be equal zero.
> I don't understand that how a charged system can be simulated using periodic boundary condition.
> No need to add conterion?
> Could you please tell me why? Sorry to disturd you and I look forward to your answer.
> Best wishes,
> Dandan Yuan
> Nanjing University
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Received on Sun Jun 08 2014 - 03:30:02 PDT
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