title: Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange.
abstract: Combined quantum mechanics/molecular mechanics (QM/MM) plays an important role in multiscale simulations of biological systems including enzymes. The adaptive-partitioning (AP) schemes surpass the conventional QM/MM methods in that they allow the on-the-fly, smooth exchange of particles between QM and MM subsystems in molecular dynamics simulations, leading to a seamless and dynamic integration of the QM and MM realms. Originally developed for simulating ion solvation in bulk solutions, the AP schemes have recently been extended to the treatment of proteins, fostering applications in the simulations of enzymes. The present contribution provides a detailed account of the AP schemes. We delineate the background of the algorithms and their parallel implementation, as well as offer practical advice and examples for their applications in the simulations of biological systems.
authors: University of Colorado Denver, Denver, CO, United States.
authors: A
authors: A
authors: Duster
authors: University of Colorado Denver, Denver, CO, United States.
authors: C
authors: C
authors: Garza
authors: University of Colorado Denver, Denver, CO, United States. Electronic address: hai.lin@ucdenver.edu.
authors: H
authors: H
authors: Lin
mesh_terms: D000465:Algorithms; D000818:Animals; D006801:Humans; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012996:Solutions / Q000737:chemistry*
chemical_list: D011506:Proteins; D012996:Solutions
keywords: Adaptive partitioning; Combined QM/MM; Many-body expansion; Molecular dynamics; On-the-fly reclassification; Parallel implementation; Particle exchange