[gmx-users] non-neutral system

[Faezeh Pousaneh]

Thank you guys.

Johanns, I think one must add counter-ions by himself (which I do not
want), as written here
http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge





Best regards


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
>
> Johannes
>
>
>
> On 06.11.2017 11:57, João Henriques wrote:
>
>> ​Hi,
>>
>> 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.
>>
>> Cheers,
>> J
>>
>> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
>> 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?
>>>
>>> If I use counter-ions to neutralize the system, I am afraid the
>>> properties
>>> I am looking for (viscosity) will be influenced.
>>>
>>> Best regards
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