What is the principle or methods to designate the QM calculation region

[iweqouwi]

What is the principle or methods to designate the QM calculation region

[lohedges]

Hi there,

This is a question that can only fully be answered using knowledge about the system you intend to simulate. For our purposes, we are primarily interested in binding free-energy calculations, so would treat the ligand at the QM (or ML) theory level, possibly also including important residues within the binding pocket. This GROMACS tutorial gives a good overview of things to consider. When treating only part of a molecule at the QM level, e.g. specific residues in a protein, then it is usually good practice to cut the QM/MM region along a carbon-carbon bond. Our implementation has automatic handling for link-atoms and will warn the user if this is not the case.

Cheers.

[lohedges]

Closing since this is a general QM/MM question, rather than a Sire issue.