[gmx-users] non-neutral system

[Hermann, Johannes]

In the link it says:

"Note for PME 
<http://www.gromacs.org/Documentation/Terminology/Particle_Mesh_Ewald> 
users: It is possible to use a uniform neutralizing background charge in 
PME 
<http://www.gromacs.org/Documentation/Terminology/Particle_Mesh_Ewald> 
to compensate for a system with a net background charge. There is 
probably nothing wrong with this in principle, because the uniform 
charge will not perturb the dynamics. Nevertheless, it is standard 
practice to actually add counter-ions 
<http://www.gromacs.org/Documentation/Gromacs_Utilities/genion> to make 
the system net neutral."

Hence, it is also possible without adding - right?


On 06.11.2017 12:45, Faezeh Pousaneh wrote:
> 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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>> --
>> ______________________________________
>> *Technische Universität München*
>> *Johannes Hermann, M.Sc.*
>> Lehrstuhl für Bioverfahrenstechnik
>> Boltzmannstr. 15
>> D-85748 Garching
>> Tel: +49 8928915730
>> Fax: +49 8928915714
>>
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-- 
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de
http://www.biovt.mw.tum.de/