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

preprint
submitted on 13.02.2021, 07:49 and posted on 16.02.2021, 12:43 by Vinicius Cruzeiro, Madushanka Manathunga, Kenneth M. Merz, Jr., Andreas Goetz

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, the N-methylacetamide (NMA) molecule and the photoactive yellow protein (PYP) in bulk water, 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 38x between a single GPU vs. a single CPU core and of up to 2.6x when comparing four GPUs to a single GPU. Results also reveal speedups of up to 3.5x when the API is used instead of FBI.

Funding

Elements: Software: NSCI: Efficient GPU Enabled QM/MM Calculations: AMBER Coupled with QUICK

Directorate for Computer & Information Science & Engineering

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XSEDE: eXtreme Science and Engineering Discovery Environment

Directorate for Computer & Information Science & Engineering

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History

Email Address of Submitting Author

agoetz@sdsc.edu

Institution

University of California, San Diego

Country

United States

ORCID For Submitting Author

0000-0002-8048-6906

Declaration of Conflict of Interest

The authors declare no competing financial interest.

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