Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

The
quantum mechanics/molecular mechanics (QM/MM) approach is an
essential and well-established tool in computational chemistry that
has been widely applied in a myriad of biomolecular problems in the
literature. In this publication, we report the integration of the
QUantum Interaction Computational Kernel (QUICK) program as an engine
to perform electronic structure calculations in QM/MM simulations
with AMBER. This integration is available through either a file-based
interface (FBI) or an application programming interface (API). Since
QUICK is an open-source GPU-accelerated code with multi-GPU parallelization,
users can take advantage of “free of charge” GPU-acceleration
in their QM/MM simulations. In this work, we discuss implementation
details and give usage examples. We also investigate energy conservation
in typical QM/MM simulations performed at the microcanonical ensemble.
Finally, benchmark results for two representative systems in bulk
water, the N-methylacetamide (NMA) molecule and the
photoactive yellow protein (PYP), show the performance of QM/MM simulations
with QUICK and AMBER using a varying number of CPU cores and GPUs.
Our results highlight the acceleration obtained from a single or multiple
GPUs; we observed speedups of up to 53× between a single GPU
vs a single CPU core and of up to 2.6× when comparing four GPUs
to a single GPU. Results also reveal speedups of up to 3.5× when
the API is used instead of FBI.