Theoretical and Computational Chemistry

QM/MM Simulations on NVIDIA and AMD GPUs

Authors

Abstract

We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra operations. General performance improvements to the QUICK GPU code are also presented. Benchmarks carried out on NVIDIA V100 and AMD MI100 cards display similar performance on both hardware for standalone HF/DFT calculations with QUICK and QM/MM molecular dynamics simulations with QUICK/AMBER. Furthermore, with respect to the QUICK/AMBER release version 21, significant speedups are observed for QM/MM molecular dynamics simulations. This significantly increases the range of scientific problems that can be addressed with open-source QM/MM software on state-of-the-art computer hardware.

Content

Thumbnail image of Manuscript_AMD.pdf

Supplementary material

Thumbnail image of qmmm_inputs.zip
Input files for QM/MM simulations
This zip file contains input files for sander program of AMBER MD package that were used for the QM/MM simulations reported in the paper.