[gmx-users] non-neutral system

[Justin Lemkul]

On 11/6/17 6:03 AM, Hermann, Johannes wrote:
> Hey Joao,
>
> are you sure? I think PME will introduce a neutralizing background 
> charge?
>

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.

-Justin

> 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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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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