[gmx-users] QM/MM with Orca

[Marcos Veríssimo Alves]

Hi all,

I have managed to compile Gromacs (2016 and 5.0.7) and run a simple QM/MM
calculation with Orca as the QM engine, a MD run for a small peptide in
vacuum. (If anyone is interested, I can share the procedure, adapted from a
tutorial I found on the web.) However, the question I have is not specific
to the Gromacs/Orca combination, but a bit more general.

Now I'd like to solvate the peptide in water and perform a QM/MM run. It
seems fairly simple if all water molecules are treated classically (please
correct me if I'm wrong): the peptide will be QM, the waters are MM and no
link atoms will be necessary. The coupling between the two regions will be
handled by Gromacs and Orca via the polarization of the QM region by point
charges and LJ. Am I right?

Now, if the some of the water molecules are to be treated
quantum-mechanically, there's the problem of molecules crossing the
boundary of the quantum region. With a Google search, I stumbled upon the
FIRES method (Salahub et al, Molecules 2015, 20, 4780-4812, doi:
10.3390/molecules20034780), which uses restraints (a simple quadratic
potential) for keeping QM water molecules within a certain sphere around
the QM molecule inside the sphere, while keeping MM molecules outside it.

Is this method implemented in Gromacs, or could it be implemented for the
QM and MM water molecules via specification of restraints in the .itp files?

Thanks in advance,

Marcos