Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations

Abstract

In many applications of multilevel/multiscale methods, an active zone must be modeled by a high-level electronic structure method, while a larger environmental zone can be safely modeled by a lower-level electronic structure method, molecular mechanics, or an analytic potential energy function. In some cases though, the active zone must be redefined as a function of simulation time. Examples include a reactive moiety diffusing through a liquid or solid, a dislocation propagating through a material, or solvent molecules in a second coordination sphere (which is environmental) exchanging with solvent molecules in an active first coordination shell. In this article, we present a procedure for combining the levels smoothly and efficiently in such systems in which atoms or groups of atoms move between high-level and low-level zones. The method dynamically partitions the system into the high-level and low-level zones and, unlike previous algorithms, removes all discontinuities in the potential energy and force whenever atoms or groups of atoms cross boundaries and change zones. The new adaptive partitioning (AP) method is compared to Rode's "hot spot" method and Morokuma's "ONIOM-XS" method that were designed for multilevel molecular dynamics (MD) simulations. MD simulations in the microcanonical ensemble show that the AP method conserves both total energy and momentum, while the ONIOM-XS method fails to conserve total energy and the hot spot method fails to conserve both total energy and momentum. Two versions of the AP method are presented, one scaling as O(2N) and one with linear scaling in N, where N is the number of groups in a buffer zone separating the active high-level zone from the environmental low-level zone. The AP method is also extended to systems with multiple high-level zones to allow, for example, the study of ions and counterions in solution using the multilevel approach.

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials

“…Adaptive resolution methods address this issue by dynamically assigning molecules HR or LR character based on their proximity to the active site. [6][7][8][9][10][11][12][13] Generally, this procedure involves a transition region that connects smoothly the active and environment regions (T-region, Figure 1). The solvent molecules in the T-region have partial HR and partial LR character, and the description of each solvent molecule s smoothly changes from HR to LR (or vice versa) as it moves across the region.…”

“…The novel approach is an extension of current adaptive QM/MM formulations, and is very general in that it can be combined with many of the available flavors. 6,8,9 This paper is organized as follows. In Section 2 we introduce the theory behind adaptive dual-resolution simulations.…”

Understanding cross‐boundary events in ONIOM QM:QM' calculations

“…29 One problem is that the present QM:QM' scheme also leads to error in reaction energies beyond the errors in the QM' method, and these errors should not propagate into the ONIOM-XR scheme. The design of ONIOM-XR is a therefore an elaborate project, and has not been attempted as part of the present study.…”

Investigating Atmospheric Sulfuric Acid–Water–Ammonia Particle Formation Using Quantum Chemistry

“…These methods include the resolution-ofidentity approximations, which have recently been used in atmospheric studies for example by Fliegl et al [81] and Kurtén et al [70], and the density fitting approximation, which has been successfully applied by Nadykto et al [102] to the vibrational spectra of sulfuric acid monohydrate and formic acid dimer clusters. Intriguing possibilities are also offered by various QM/MM (Quantum Mechanics/Molecular Mechanics) methods and fragmentation or embedding models, see for example Heyden et al [103] and Dahlke and Truhlar [104] for recent applications to water clusters, and Falsig et al [105] for an atmospherically relevant study of phenol-water cluster reactions.…”