[gmx-users] non-neutral system
jalemkul at vt.edu
Mon Nov 6 12:50:43 CET 2017
On 11/6/17 6:03 AM, Hermann, Johannes wrote:
> Hey Joao,
> are you sure? I think PME will introduce a neutralizing background
It does. Whether or not it's appropriate is another matter. For
homogeneous systems, it's fine, but if dealing with something
heterogeneous like a membrane, there are serious artifacts in this approach.
> All the best
> On 06.11.2017 11:57, João Henriques wrote:
>> You shouldn't use PME without neutralizing the system's charge. It's a
>> limitation of the Ewald summation. Take a look at the literature for
>> further details.
>> I don't know much about viscosity, so I'll leave that for someone else.
>> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
>>> 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
>>> they are wrong (total columb potential is negative value which must be
>>> positive). Any idea why?
>>> If I use counter-ions to neutralize the system, I am afraid the
>>> I am looking for (viscosity) will be influenced.
>>> Best regards
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
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