From: Hyonseok Hwang (danggi_at_northwestern.edu)
Date: Wed May 17 2006 - 01:31:08 CDT
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
Thanks a lot.
-- ======================================= Hyonseok Hwang Postdoctoral Fellow Department of Chemistry Northwestern University 2145 Sheridan Rd. Evanston, IL 60208-3113 USA --------------------------------------- Tel:(847)467-4987(O) Email:danggi_at_northwestern.edu =======================================
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