Ron Levy group

Exploring
molecular
landscapes

Statistical Thermodynamics

Chemistry 5302

Fall 2017

Time and Location:

  • Tues/Thurs, 5:30PM, SERC 702

Contacts:

Syllabus:

  • pdf
  • MQ = Donald McQuarrie, "Statistical Mechanics" (Harper Collins 1976)
  • KD = Ken Dill and Sarina Bromberg, "Molecular Driving Forces" (Garland Science 2nd ed, 2011)

I. Equilibrium

Date Topic Lecture Slides
1. 8/29 Thermodynamics review - MQ Chapter 1 pdf ppt
2. 8/31, 9/5 Canonical ensemble - MQ Chapter 2 pdf ppt
Problem Set 1 pdf
Problem Set 1 Solutions pdf
3. 9/7, 9/12 Fluctuations and other ensembles - MQ Chapter 3 pdf ppt
Problem Set 2 pdf
Problem Set 2 Solutions pdf
4. 9/14 Classical statistical mechanics - MQ Chapter 7 pdf ppt
Problem Set 3 pdf
Problem Set 3 Solutions pdf
5. 9/14, 9/19 Ideal Gas - MQ Chapter 5 pdf ppt
6. 9/19, 9/21 Imperfect gases - MQ Chapter 12 pdf ppt
7. 9/26, 9/28 Liquids - MQ Chapter 13 pdf ppt
8. 10/3,10/5,10/10 Chemical Equilibria - MQ Chapter 9, KD Chapter 13 pdf ppt
9. 10/12 Binding Equilibria: DDM,FEP,BEDAM - Notes pdf ppt


II. Computational Methods

Date Topic Lecture Slides
10. 10/17 Intermolecular interactions, potential energy functions - Notes pdf ppt
11. 10/19 Solvation Models - Notes pdf ppt
12. 10/24 Simulation Methods (MD, MC) - Notes pdf ppt
13. 10/26 Advanced conformational sampling - Notes pdf ppt
14. 10/31 Binding Equilibria II: DDM,FEP,BEDAM - Notes pdf ppt


III. Computer Labs with Lectures

Date Topic Lecture Slides
15. 11/2 Introduction to Maestro and Impact pdf
16. 11/7,11/9,11/14 Lab 1 - Water pdf
17. 11/16 Binding Free Energy Calculation & Docking pdf ppt
18. 11/28,11/30 Lab 2 - Glide & BEDAM pdf
19. 12/5 DDM & FEP - Notes pdf ppt
20. 12/7,12/12 Lab 3 - DDM & FEP pdf