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Cambridge, MA - April 29th, 2020

QSimulate technology enables groundbreaking advances in quantum mechanics/molecular mechanics (QM/MM) simulations for large protein modeling

QSimulate technology enables groundbreaking advances in quantum mechanics/molecular mechanics (QM/MM) simulations for large protein modeling
graphical abstract
A new publication from RIKEN has described a native integration of the highly efficient QSimulate-QM software and RIKEN’s GENESIS molecular dynamics (MD) program, achieving unprecedented throughput for the simulations of large protein reactions. High throughput suggests a broadened scope of applicability for QM/MM calculations going forward. Questions of drug discovery and materials development that have previously been beyond the reach of QM due to insufficient turnaround now appear to be within our grasp.
Using the integrated software, the authors demonstrated 1.4 ns of MD simulation per day for a protein system consisting of ∼30,000 atoms including 35 atoms treated by a semi-empirical QM approach (DFTB). This throughput is nearly an order of magnitude improvement compared to existing software solutions. They also presented a throughput of about 40 ps/day using a fully QM approach (B3LYP). This enabled the authors to accurately investigate a representative enzymatic reaction.
The article, entitled Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations, has been published in The Journal of Physical Chemistry B on April 29th, 2021 as part of the virtual special issue “Computational Advances in Protein Engineering and Enzyme Design.”