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Lecture

Integration Algorithms for Molecular Dynamics: Verlet Algorithm

In course

PHYS-403: Computer simulation of physical systems I

The two main topics covered by this course are classical molecular dynamics and the Monte Carlo method. ...

Description

This lecture covers integration algorithms for Molecular Dynamics, focusing on the Verlet algorithm. It explains the Position Verlet method, Velocities with Verlet, Leap-frog Verlet, and Velocity Verlet. The lecture details the advantages of the Position Verlet algorithm and discusses the accuracy and order of the velocity calculations. Examples, such as the Harmonic oscillator, are used to illustrate the concepts. Additionally, the Leap-frog Verlet method is explained, showing its equivalence to the Position Verlet algorithm. The Velocity Verlet algorithm is also presented, highlighting its sequence and equivalence with the Position Verlet method.

Instructor

Alfredo Pasquarello

Alfredo Pasquarello studied physics at the Scuola Normale Superiore of Pisa and at the University of Pisa, obtaining their respective degrees in 1986. He obtained a doctoral degree at the EPFL in 1991 with a thesis on Multiphoton Transitions in Solids . Then, he moved to Bell Laboratories at Murray Hill (New Jersey), where he carried out postdoctoral research on the magnetic properties of carbon fullerenes. In 1993, he joined the Institute for Numerical Research in the Physics of Materials (IRRMA), where his activity involved first-principles simulation methods. In 1998, he was awarded the EPFL Latsis Prize for his research work on disordered silica materials. Succeeding in grant programs of the Swiss National Science Foundation, he then set up his own research group at IRRMA. In July 2003, he is appointed Professor in Theoretical Condensed Matter Physics at EPFL. Currently, he leads the Chair of Atomic Scale Simulation.

Official source

Related concepts (9)

Verlet integration

Verlet integration (vɛʁˈlɛ) is a numerical method used to integrate Newton's equations of motion. It is frequently used to calculate trajectories of particles in molecular dynamics simulations and computer graphics. The algorithm was first used in 1791 by Jean Baptiste Delambre and has been rediscovered many times since then, most recently by Loup Verlet in the 1960s for use in molecular dynamics. It was also used by P. H. Cowell and A. C. C.

Symplectic integrator

In mathematics, a symplectic integrator (SI) is a numerical integration scheme for Hamiltonian systems. Symplectic integrators form the subclass of geometric integrators which, by definition, are canonical transformations. They are widely used in nonlinear dynamics, molecular dynamics, discrete element methods, accelerator physics, plasma physics, quantum physics, and celestial mechanics. Symplectic integrators are designed for the numerical solution of Hamilton's equations, which read where denotes the position coordinates, the momentum coordinates, and is the Hamiltonian.

Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.

Numerical integration

In analysis, numerical integration comprises a broad family of algorithms for calculating the numerical value of a definite integral, and by extension, the term is also sometimes used to describe the numerical solution of differential equations. This article focuses on calculation of definite integrals. The term numerical quadrature (often abbreviated to quadrature) is more or less a synonym for numerical integration, especially as applied to one-dimensional integrals.

Molecular modelling

Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.

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