Lessons

Molecular modeling

Material that we have developed to teach theory, methods, and practices of molecular simulation

Lectures (Click to expand)

Powerpoint lectures developed when teaching CE 530 Molecular Simulation, dating from 2000 with very few updates since.

The pdf files are more likely to preserve the format and fonts of the original slides; the Powerpoint files are provided to allow users to edit and update the content. Zip archives collecting all pdf and ppt files are included at the bottom.

Introduction pdf ppt
Physical quantities, hard-sphere MD pdf ppt
Common elements of a molecular simulation pdf ppt
Statistical mechanics pdf ppt
Monte Carlo integration and importance sampling pdf ppt
Markov processes pdf ppt
Monte Carlo simulation pdf ppt
Simple biasing methods pdf ppt
Molecular dynamics simulation pdf ppt
Dynamical properties pdf ppt
Molecular dynamics in other ensembles pdf ppt
Molecular models pdf ppt
Long-range forces and Ewald sums pdf ppt
Dielectrics and reaction field method pdf ppt
Beyond atoms: Simulating molecules pdf ppt
Free-energy calculations: Basics pdf ppt
Free-energy calculations: Distribution functions, precision, and accuracy pdf ppt
Phase equilibria pdf ppt
Histogram reweighting methods pdf ppt
Chain-molecule sampling techniques pdf ppt
Symmetric MD integrators pdf ppt
Non-equilibrium molecular dynamics pdf ppt
Efficiencies and parallel methods pdf ppt

Archive of lectures 1-8

Archive of lectures 9-15

Archive of lectures 16-23

Note that lecture numbering used in presentation files does not match the numbering used here.

Text (Click to expand)

Text documents that provide more detailed explanations of some of the concepts presented in the Powerpoint lectures.

Physical quantities in molecular simulations pdf
Error analysis pdf
Statistical mechanics pdf
Basic molecular dynamics pdf
Hard-sphere molecular dynamics pdf
Markov processes pdf
Monte Carlo simulation pdf
Simple biasing methods pdf
Long-range forces pdf

Etomica Java code included in some of these files is not up-to-date with the classes currently making up the framework.

Elementary quantum chemistry and machine learning

Lecture materials from a special-topics course on "Modeling Potential Energy Surfaces", taught in Spring 2024. The course covers computational chemistry as applied to calculation of potential energies, and modeling of potential energy surfaces using force fields and machine-learning methods.

CE 500 lecture material

About half of the course deals with basic concepts and methods of quantum chemistry with a focus on calculation of interatomic/molecular energies. Topics of machine learning occupy the last quarter of the course. Only basic concepts and methods of machine learning are presented, as time ran out before we got to detailed discussions of applications to modeling potential energy surfaces.

Mathematica is used extensively as an aid to development and demonstration of some of the concepts presented in the course.

The pdf files are printed from the Powerpoint slides and are more likely to preserve the format and fonts of the original slides. The zip archives include the original Powerpoint files and Mathematica notebooks (.nb) that were used to produce some of the figures in the slides, and to reinforce lessons in class.

Zip archives collecting ppt and nb files for multiple lectures are included at the bottom, to make downloading the entire set a bit easier. Host file-size limits prevent grouping these into larger collections.