Introduction to Molecular Modeling and Simulation

URL study guide

https://tue.osiris-student.nl/onderwijscatalogus/extern/cursus?cursuscode=2MMN40&collegejaar=2025&taal=en

Description

We intend to give an overview of computational tools that are currently used to study the equilibrium properties of molecular substances. The discussion is limited to classical many-body systems. The following topics will be covered: Newtonian mechanics and Hamiltonian formalism; simplecticity and numerical integrators; statistical mechanics and phase space observables; thermodynamical ensembles; coarse graining. The course combines the discussion of theoretical aspects in the lectures with direct practical implementation in a modular molecular dynamics simulator during instructions.

The course will consist of a combination of lectures, programming examples, and practical simulation assignments/projects. All programming examples will be given using python. Python is also the only accepted programming language for the assignments.

 

Objectives

Describe classical molecular processes in terms of Newtonian mechanics, understand the many-body problem in terms of Hamiltonian formalism, solve the associated differential equations with numerical algorithms, extract thermodynamic properties from phase space trajectories using statistical mechanics, implement a small-scale molecular dynamics simulation tool in python, demonstrate collaborative design of scientific computing tools.

Method of Assessment

Written report