Towards chemically accurate QM/MM simulations on GPUs

Publication date: Available online 16 January 2020Source: Journal of Molecular Graphics and ModellingAuthor(s): Ádám Jász, Ádám Rák, István Ladjánszki, Gábor János Tornai, György CsereyAbstractComputational chemistry simulations are extensively used to model natural phenomena. To maintain performance similar to molecular mechanics, but achieve comparable accuracy to quantum mechanical calculations, many researchers are using hybrid QM/MM methods. In this article we evaluate our GPU-accelerated ONIOM implementation by measurements on the crambin and HIV integrase proteins with different size QM model systems. We demonstrate that by using a larger QM region, a better energy accuracy can be achieved at the expense of simulation time. This trade-off is important to consider for the researcher running QM/MM calculations. Furthermore, we show that the ONIOM energy monotonically approaches the pure quantum mechanical energy of the whole system. The experiments are made feasible by utilizing the cutting-edge BrianQC quantum chemistry module for Hartree-Fock level SCF and our GPU-accelerated MMFF94 force field implementation for molecular mechanics calculations.Graphical abstract
Source: Journal of Molecular Graphics and Modelling - Category: Molecular Biology Source Type: research