[gmx-users] non-neutral system
jalemkul at vt.edu
Mon Nov 6 12:52:04 CET 2017
On 11/6/17 5:50 AM, Faezeh Pousaneh wrote:
> I have a system containing similar charged atoms. So the total charge is
> not zero.
> Simulation results with cut-off coulomb seems reasonable, but using PME
> they are wrong (total columb potential is negative value which must be
> positive). Any idea why?
Cutoff electrostatics are a poor method to use. State of the art decades
ago, but PME is the de facto standard. Why should the total
electrostatic energy be positive in your case? What exactly is your system?
> If I use counter-ions to neutralize the system, I am afraid the properties
You may not necessarily need counterions, but you'll have to explain
more about what your system is (see my other post regarding the
neutralizing background plasma).
> I am looking for (viscosity) will be influenced.
> Best regards
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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