[gmx-developers] GROMACS 4.0.7 QM/MM exclusions

Berk Hess hess at cbr.su.se
Fri Nov 19 11:08:31 CET 2010

On 11/19/2010 08:21 AM, Gerrit Groenhof wrote:
>  Hi,
> 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.
> Gerrit
Isn't the energy group exclusion that we discussed a simple solution?
We could do something like that automated as well (if it works).

> 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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