Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.


Journal Article

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Full Text

Duke Authors

Cited Authors

  • Shen, L; Wu, J; Yang, W

Published Date

  • October 2016

Published In

Volume / Issue

  • 12 / 10

Start / End Page

  • 4934 - 4946

PubMed ID

  • 27552235

Pubmed Central ID

  • 27552235

Electronic International Standard Serial Number (EISSN)

  • 1549-9626

International Standard Serial Number (ISSN)

  • 1549-9618

Digital Object Identifier (DOI)

  • 10.1021/acs.jctc.6b00663


  • eng