[gmx-users] non-neutral system
joao.m.a.henriques at gmail.com
Mon Nov 6 13:06:28 CET 2017
I just meant that from a purely theoretical point of view, it needs to be
neutral. This has to do with the convergence of the outer infinite series,
as the paper Micholas linked clearly states. I sincerely hope I'm not
botching this up, but this is the conclusion I've withdrawn from reading
the literature. Now, if the software implementation contains some tricks to
account for this, that I'm not familiar with and will therefore leave that
discussion for someone else more acquainted with it.
On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
J.Hermann at lrz.tu-muenchen.de> wrote:
> Hey Joao,
> are you sure? I think PME will introduce a neutralizing background charge?
> 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 PME
>>> 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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