[gmx-developers] Question about MM point charges in QM/MM calculation

[Berk Hess]

Yes, but what I am trying to tell you is that the brick in unphysical.
But if you really need it for neutrality, it might be the best option 
you have.

I don't know if the code Gerrit makes produces the brick like shape 
correctly.

Berk

Pia Toelle wrote:
> Okay, now I understand.
>
> I do not need the images of the charges. I just need the "rectangular
> brick". The periodic boundary conditions are handled in the QM
> calculation by DFTB+ (www.dftb-plus.info).
>
> As I told in my first Email, I do not use neutral well defined charge
> groups (due to the system I am using), therefor I am getting into
> trouble   with the cut-off defined MM-charges (as the routine depends
> much on the charge group definition). I end up with a non neutral total
> charges (from all point charges), that also fluctuates a lot from one
> step to the next.
>
> Pia
>
>
>
> Berk Hess wrote:
>   
>> But I was trying to say that with PBC it does not make sense to use all
>> MM charges.
>> Since your system is periodic all charges are periodically repeated in
>> all directions.
>> To do this correctly you would need infinitely many charges.
>> You could use the minimum image convention, but then you will have a
>> rectangular brick
>> of MM charges. When a charge on the boundary moves slightly, it will
>> suddenly jump
>> to the other side.
>>
>> I would suggest to simply use a cut-off of nearly half the smallest box
>> size.
>> Then you will have a nearly spherical group of charges.
>>
>> Berk
>>
>> Pia Toelle wrote:
>>     
>>> Thanks for your help!
>>>
>>> I do have pbc! And I would like to include all non-QM-atoms as MM point
>>> charges. As I am using DFTB, a big number of point charges are no
>>> problem.
>>> What's about the last comment? Is it possible to put all cut-off's to
>>> zero and where? Are you talking about changes in the code or just in the
>>> mdp-file?
>>> Or maybe I will try the changes Gerrit proposed.
>>>
>>> Pia
>>>
>>> Berk Hess wrote:
>>>  
>>>       
>>>> But in case of no pbc, couldn't you just run with no cut-off (all
>>>> cut-offs set to zero)
>>>> and automatically get all MM charges?
>>>> Since MM should be cheap compared to QM this should not be
>>>> computationally expensive.
>>>>
>>>> Berk
>>>>
>>>>     
>>>>         
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