High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM-Reference-Cited by-同舟云学术

High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM

Published:2025-04-02 Issue:8 Volume:21 Page:4016-4029
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Yagi Kiyoshi¹²^ORCID,Gunst Klaas³,Shiozaki Toru³,Sugita Yuji¹⁴⁵^ORCID

Affiliation:

1. Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan

2. Department of Chemistry, Institute of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan

3. Quantum Simulation Technologies, Inc.

4. Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

5. Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan

Funder

RIKEN

Japan Society for the Promotion of Science

Publisher

American Chemical Society (ACS)

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00163

Reference91 articles.

1. Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization

2. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

3. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH₃Cl + Cl⁻ exchange reaction and gas phase protonation of polyethers

4. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

5. IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states