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Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

ABSTRACT: It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.

SUBMITTER: Yamashita T

PROVIDER: S-EPMC4120847 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

Yamashita Takefumi T Peng Yuxing Y Knight Chris C Voth Gregory A GA

Journal of chemical theory and computation 20121201 12

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between parti ...[more]

PMID: 25100924

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Project description:The molecular simulation of chemical reaction equilibrium (CRE) is a challenging and important problem of broad applicability in chemistry and chemical engineering. The primary molecular-based approach for solving this problem has been the reaction ensemble Monte Carlo (REMC) algorithm [Turner et al. Molec. Simulation2008, 34, (2), 119-146], based on classical force-field methodology. In spite of the vast improvements in computer hardware and software since its original development almost 25 years ago, its more widespread application is impeded by its computational inefficiency. A fundamental problem is that its MC basis inhibits the implementation of significant parallelization, and its successful implementation often requires system-specific tailoring and the incorporation of special MC approaches such as replica exchange, expanded ensemble, umbrella sampling, configurational bias, and continuous fractional component methodologies. We describe herein a novel CRE algorithm (reaction ensemble molecular dynamics, ReMD) that exploits modern computer hardware and software capabilities, and which can be straightforwardly implemented for systems of arbitrary size and complexity by exploiting the parallel computing methodology incorporated within many MD software packages (herein, we use GROMACS for illustrative purposes). The ReMD algorithm utilizes these features in the context of a macroscopically inspired and generally applicable free energy minimization approach based on the iterative approximation of the system Gibbs free energy function by a mathematically simple convex ideal solution model using the composition at each iteration as a reference state. Finally, we additionally describe a simple and computationally efficient a posteriori method to estimate the equilibrium concentrations of species present in very small amounts relative to others in the primary calculation. To demonstrate the algorithm, we show its application to two classic example systems considered previously in the literature: the N2-O2-NO system and the ammonia synthesis system.

Dataset Information

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

Publications

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

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