Lecture

Integration Algorithms for Molecular Dynamics: Verlet Algorithm

Graph Chat

Chat with Graph Search

Ask any question about EPFL courses, lectures, exercises, research, news, etc. or try the example questions below.

DISCLAIMER: The Graph Chatbot is not programmed to provide explicit or categorical answers to your questions. Rather, it transforms your questions into API requests that are distributed across the various IT services officially administered by EPFL. Its purpose is solely to collect and recommend relevant references to content that you can explore to help you answer your questions.

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 (12)

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.

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.

Integral

In mathematics, an integral is the continuous analog of a sum, which is used to calculate areas, volumes, and their generalizations. Integration, the process of computing an integral, is one of the two fundamental operations of calculus, the other being differentiation. Integration started as a method to solve problems in mathematics and physics, such as finding the area under a curve, or determining displacement from velocity. Today integration is used in a wide variety of scientific fields.

Molecular design software

Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g

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.

Related lectures (62)

Molecular dynamics under constraints

Explores molecular dynamics simulations under holonomic constraints, focusing on numerical integration and algorithm formulation.

Classical Molecular Dynamics: Simulation and Integration Algorithms

Explores classical molecular dynamics simulations, integration algorithms, and trajectory accuracy.

Constraints in Molecular Dynamics: General Method and SHAKE Algorithm

Covers the general method and SHAKE algorithm for constraints in Molecular Dynamics.

Molecular dynamics and integrators

Explores molecular dynamics, integrators, trajectory generation, and error monitoring in atomistic modeling.

Molecular Dynamics Basics