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

Gerrit Groenhof ggroenh at gwdg.de
Sat Jan 31 16:06:08 CET 2009


We did a gmx-dftb interface that used function calls from the linked  
dftb librarysome time ago. That was in 3.3.3, but I never found the  
time to pt it in 4. ALso I remember some compilation issues with the  
dftb code on 64 bit machines. I can send you the code if you're  

For QM/MM the MM atoms are indeed set with the cut-off options.  
Although for dftb it is not very difficult, I have never found the  
time or need to complete the ewald implementation.  To avoid  
duplications, I suggest we finish the PME implementation for the DFTB  
code together. Contacting me off-list  is probably more convenient if  
you are interested.



On 30 Jan 2009, at 18:09, Pia Toelle wrote:

> Hello.
> I have got some questions concerning the MM-atom-list in a QM/MM
> calculation.
> We do QM-MM calculations using the Gaussian interface (gromacs-3.3.3),
> but modified the code to be able to use DFTB instead of Gaussian
> (www.dftb.org).
> Our (MM-)system is a SiO2-surface (with periodic boundary condition;  
> full).
> We use PME and DO NOT (!) define proper charge groups for the surface
> structure, every atom forms its own charge group. Number of MM atoms  
> ~1900.
> (The proper definition of charge groups in our system is not obvious  
> or
> even impossible, as it is a solid and a periodic system)
> We noticed, that the MM system considered in the QM calculation does  
> not
> consist of the entire MM system. The point charges
> (mm->xMM[i][..],mm->MMcharges[i]) that are written to input.com (by
> qm_gaussian.c) are only those of the MM atoms in the vicinity of the  
> QM
> atoms. The list of MM atoms in the vicinity of the QM-zone is set (as
> far as we can see) using the neighbor-search algorithm depending  
> also on
> the charge groups (in ns5_core.c). Please correct me if I am wrong at
> some point.
> Is it right, that the cut-off for the QM/MM - neighbor search is set  
> by
> 'rcoulomb' in the mdp-file? Or 'rlist'?
> Anyhow, we would like to print out all (!) MM atoms (and their  
> charges).
> How to solve this problem?
> Is there a simple way to put all MM atoms in the mm list? And please
> tell me if a change of the (t_MMrec)-variable mm could cause problems
> for the MM-part of the routine or is  the (t_MMrec)-variable mm only
> used in the QM part.
> Or would it be possible to print out all MM atoms + charges at an  
> other
> point in the program? Where?
> I am grateful for any helpful information or idea.
> Thanks in advance.
> Pia Toelle
> Uni Bremen
> Am Fallturm 1
> 28359 Bremen
> Germany
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Gerrit Groenhof
MPI biophysical chemistry

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