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

Pia Toelle pia.toelle at bccms.uni-bremen.de
Tue Feb 3 16:16:01 CET 2009

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.


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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