Multiscale reactive molecular dynamics

Abstract

Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

Acid activation mechanism of the influenza A M2 proton channel

“…The PT PMF in the regions outside the His37-Trp41 tetrad region (Fig. 1A) was calculated using the MS-RMD method (84)(85)(86)(87) implemented with the LAMMPS MD package (lammps.sandia.gov) (88). Umbrella sampling was used and the same CV was used, except that in the MS-RMD simulation the excess proton CEC is given by (89) r CEC = X N i c 2 ir i coc , [4] wherer i coc is the coordinates of the center of charge of the ith diabatic state.…”

Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations

“…In addition, because the accuracy of the potential model is essential for the success of MD simulations, the parameterization method is very important. Recently, Knight, Lindberg, and Voth [26] proposed that the force matching method is a promising method for directly determining the force field parameters from ab initio MD simulation data.…”

Dynamic behavioral assessment model based on Hebb learning rule

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