Publication

A fully-polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework

2024

Abstract

In this work, we present the development of a fully-polarizable KS-DFT/AMOEBA embedding scheme for delocalized basis sets such as plane-waves and real-space grids. The augmented problem of electron spill-out inherent to a polarizable QM/MM implementation with plane-wave basis sets is addressed and the periodicity for the MM subsystem is taken into account, as implemented in the Tinker-HP software. We discuss the software design and how computational efficiency is enabled through the interoperable multiscale simulation framework MiMiC. The implementation is validated on QM/MM energies for dimer systems and a quantitative assessment of molecular dipoles of embedded solutes in order to estimate the magnitude of errors related to the damping parameters used in the model.

Official source

https://infoscience.epfl.ch/entities/publication/e1f3247c-0a2f-4fac-bf4a-efd301b60197

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2024

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/e1f3247c-0a2f-4fac-bf4a-efd301b60197

About this result

Related concepts (23)

Basis set (chemistry)

In theoretical and computational chemistry, a basis set is a set of functions (called basis functions) that is used to represent the electronic wave function in the Hartree–Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer. The use of basis sets is equivalent to the use of an approximate resolution of the identity: the orbitals are expanded within the basis set as a linear combination of the basis functions , where the expansion coefficients are given by .

Molecular mechanics

Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.

Force field (chemistry)

In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.

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A fully-polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework

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