[gmx-developers] GROMACS 4.0.7 QM/MM exclusions

Gerrit Groenhof ggroenh at gwdg.de
Fri Nov 19 08:21:30 CET 2010


This is a problem when the QM atoms are not in the same topology. I have 
not yet found a satisfactory solution, also because a very easy 
work-around is to put all QM atoms into the same topology file.

But I agree that´s not the best solution and this needs to be solved.


On 11/19/2010 01:01 AM, Lee-Ping wrote:
> ver, there is still another problem.  The entire moltype struct is
> not actually copied at line 1000; line 1004 copies the exclusions over
> and the comment claims that "this is the only thing that needs to be
> modified for QMMM."  But this is untrue; generate_qmexcl_moltype not
> only modifies the exclusions, but also deletes entries from the bonded
> interactions (ilist) within moltype!
> This will modify the bonded interactions for the MM molecules if they
> were originally the same type as the QM molecules.  I have verified
> this, and it's a serious problem that will break QM/MM calculations
> where QM and MM molecules start from the same type (e.g. if they are
> both water).
> I think this is a bug that can be avoided by copying over the ilist
> struct (or the entire moltype struct) when the QM/MM moltype is created,
> but no such functions seem to be built-in to GROMACS 4.0.7.  I could
> write these functions myself if people would find it useful.  Please

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