[gmx-users] non-neutral system

Justin Lemkul jalemkul at vt.edu
Mon Nov 6 12:52:04 CET 2017

On 11/6/17 5:50 AM, Faezeh Pousaneh wrote:
> Hi,
> 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.
Assistant Professor
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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