QM/MM
simulations have become an indispensable tool in many chemical
and biochemical investigations. Considering the tremendous degree
of success, including recognition by a 2013 Nobel Prize in Chemistry,
are there still “burning challenges” in QM/MM methods,
especially for biomolecular systems? In this short Perspective, we
discuss several issues that we believe greatly impact the robustness
and quantitative applicability of QM/MM simulations to many, if not
all, biomolecules. We highlight these issues with observations and
relevant advances from recent studies in our group and others in the
field. Despite such limited scope, we hope the discussions are of
general interest and will stimulate additional developments that help
push the field forward in meaningful directions.