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

Authors: Goetz, Andreas W.; Manathunga, Madushanka; Kenneth M. Merz, Jr.;

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

Abstract

The goal of our project is to improve our software cyberinfrastructure for solving important molecular-level problems in catalysis, drug design, energy conversion. Combined quantum mechanical/molecular mechanical (QM/MM) models have enabled significant advances in our understanding of chemical reactivity. The shortcoming of QM/MM models when using ab initio or density functional theory (DFT) methods is the computational expense, which limits QM/MM modeling. The performance of QM methods has been greatly improved over the years through algorithmic and hardware improvements. We describe the enhancements and performance of our open-source multi-GPU enabled Quantum Interaction Computational Kernel (QUICK) QM program, which we have coupled to the AMBER molecular dynamics package to enable high-performance QM/MM simulations in condensed phase under periodic boundary conditions.

Keywords

open-source software, quantum mechanics, GPU, high-performance computing, electronic structure, performance optimization, QM/MM, DFT, molecular mechanics, molecular dynamics, QUICK, multiscale, parallelization, molecular simulations, AMBER, density functional theory

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
Green