[gmx-developers] Question about MM point charges in QM/MM calculation
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:
> I have got some questions concerning the MM-atom-list in a QM/MM
> 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
> Our (MM-)system is a SiO2-surface (with periodic boundary condition;
> 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
> (The proper definition of charge groups in our system is not obvious
> even impossible, as it is a solid and a periodic system)
> We noticed, that the MM system considered in the QM calculation does
> 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
> 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
> 'rcoulomb' in the mdp-file? Or 'rlist'?
> Anyhow, we would like to print out all (!) MM atoms (and their
> 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
> 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
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