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Lecture

Molecular Dynamics: Sampling and Thermostats

In course

MSE-421: Statistical mechanics

This course presents an introduction to statistical mechanics geared towards materials scientists. The concepts of macroscopic thermodynamics will be related to a microscopic picture and a statistical interpretation. Lectures and exercises will be compleme ...

Description

This lecture covers the use of molecular dynamics for sampling, including the generation of trajectories using Hamilton's equations, conservation laws, and the necessary conditions for detailed balance. It also discusses integrating the equations of motion, monitoring energy fluctuations, and the conservation of energy in Hamiltonian MD. The instructor explains constant-temperature molecular dynamics, the use of thermostats like Andersen thermostat, and the distinction between global and local thermostats. Additionally, deterministic and stochastic thermostats such as Nosé-Hoover and Langevin-style thermostats are presented, along with their characteristics and applications.

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Instructor

Michele Ceriotti

Michele Ceriotti received his Ph.D. in Physics from ETH Zürich in 2010. He spent three years in Oxford as a Junior Research Fellow at Merton College. Since 2013 he leads the laboratory for Computational Science and Modeling in the Institute of Materials at EPFL. His research revolves around the atomic-scale modelling of materials, based on the sampling of quantum and thermal fluctuations and on the use of machine learning to predict and rationalize structure-property relations. He has been awarded the IBM Research Forschungspreis in 2010, the Volker Heine Young Investigator Award in 2013, an ERC Starting Grant in 2016, and the IUPAP C10 Young Scientist Prize in 2018.

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Related concepts (32)

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.

Equations of motion

In physics, equations of motion are equations that describe the behavior of a physical system in terms of its motion as a function of time. More specifically, the equations of motion describe the behavior of a physical system as a set of mathematical functions in terms of dynamic variables. These variables are usually spatial coordinates and time, but may include momentum components. The most general choice are generalized coordinates which can be any convenient variables characteristic of the physical system.

Canonical ensemble

In statistical mechanics, a canonical ensemble is the statistical ensemble that represents the possible states of a mechanical system in thermal equilibrium with a heat bath at a fixed temperature. The system can exchange energy with the heat bath, so that the states of the system will differ in total energy. The principal thermodynamic variable of the canonical ensemble, determining the probability distribution of states, is the absolute temperature (symbol: T).

Grand canonical ensemble

In statistical mechanics, the grand canonical ensemble (also known as the macrocanonical ensemble) is the statistical ensemble that is used to represent the possible states of a mechanical system of particles that are in thermodynamic equilibrium (thermal and chemical) with a reservoir. The system is said to be open in the sense that the system can exchange energy and particles with a reservoir, so that various possible states of the system can differ in both their total energy and total number of particles.

Sampling (statistics)

In statistics, quality assurance, and survey methodology, sampling is the selection of a subset or a statistical sample (termed sample for short) of individuals from within a statistical population to estimate characteristics of the whole population. Statisticians attempt to collect samples that are representative of the population. Sampling has lower costs and faster data collection compared to recording data from the entire population, and thus, it can provide insights in cases where it is infeasible to measure an entire population.

Related lectures (39)

Sampling the Canonical Ensemble

Explores sampling the canonical ensemble, temperature fluctuations, extended Lagrangian, and Maxwell-Boltzmann distribution in molecular dynamics simulations.

Molecular dynamics and integrators

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

Thermodynamics and phase space sampling

Covers the computation of observables through probability distributions and the significance of efficient importance sampling in simulations.

Sampling a Probability Distribution

Explores sampling a probability distribution and structure functions in statistical analysis.

Efficiency of Sampling: Ergodicity and Autocorrelation Functions