From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Wed May 17 2006 - 09:02:47 CDT
My 2 cents:
I've never heard of this neutralizing plasma. However, if your system
is charged and the Ewald sum does not converge then you do not have well
defined energy. Without a well defined energy, you cannot have a well
defined thermodynamic state or phase space distribution function. Since
the whole point of molecular dynamics is to sample the distribution
function, even if the dynamics are "right," they are without meaning if
the energy diverges.
Hyonseok Hwang wrote:
> Dear NAMD users,
> I have a general question on the charged system. Although this is not
> directly associated with the NAMD , I hope you will let me ask this.
> Some people claim that the Ewald sum is meaningful only for a neutral
> system. They say that in a case of a charged system, we should
> neutralize the system to avoid the divergence in the Ewald sum. And in
> order to neutralize the system, people use the "uniform background
> neutralizing plasma" method with Ewald sum or particle mesh Ewald
> (PME) for charged systems. But, when I look at the equation for the
> uniform neutralizing plasma, it is just a constant (I mean,
> independent of the positions of particles) added to the Ewald sum
> equation. In fact, since what we need in the simulation, is not the
> energy, but force, I don't think that the uniform neutralizing plasma
> DOES NOT affect the dynamics AT ALL. Consequently, unless we are
> interested in the properties associated with the energy of the system,
> I don't think we have to include the neutralizing plasma term in the
> Ewald sum. I mean that we don't have to neutralize the system if we
> are interested in properties such as the structure of the system.
> As a result, if there is something wrong with my argument, please
> correct me.
> Thanks a lot.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:04 CST