Welcome to CBE 422, an introductory course on computational chemistry and molecular simulation methods.  

Time and place: The course meets on Tuesdays and Thursdays from 1:30 - 2:50 in A224, E-Quad.

Books: A recommended textbook is A. Hinchliffe, "Molecular Modelling for Beginners," 2nd ed., Wiley (2008). Other potentially useful books: B. Smit and D. Frenkel, "Understanding Molecular Simulation," 2nd ed., Academic Press (2002) and A. R. Leach, "Molecular Modelling: Principles and Applications" 2nd ed., Prentice-Hall (2001).

Grading: There will be 6 biweekly assignments (65%) and a final project (35%). Assignments are submitted electronically.

Staff: Prof. Thanos Panagiotopoulos, A317 E-Quad., x8-4591 (azp@princeton.edu). Office hours: Wed. & Fri. 2-3 pm, or by appointment.
AI: Kevin Daly, G-109 E-Quad., x8-0206 (kdaly@princeton.edu).

Web Site: The current class schedule is on the course web site, http://paros.princeton.edu/CBE422.

Tentative Course Syllabus: 1/22/2014

Lec.#

Date

Topic(s)

Reading Assignment
1 Tue 2/4 Introduction and Intermolecular Forces Ch. 1  
2 Thu 2/6 Intermolecular Forces (cont.) Ch. 2  
3 Tue 2/11 Molecular Mechanics Ch. 3,4
4 Thu 2/13 Energy Minimization, Intro to Hyperchem Ch. 5,6
5 Tue 2/18 Conformational Search, Sampling from Probability Distributions Ch. 6,7 # 1
6 Thu 2/20 Statistical Mechanical Ensembles Ch. 8, Notes  
7 Tue 2/25 Summary; Matlab Programming  
Thu 2/27 No class # 2
8 Tue 3/4 Statistical Mechanical Ensembles (cont.) Notes
9 Thu 3/6 Monte Carlo Ch. 9  
10 Tue 3/11 Grand Canonical MC # 3
11 Thu 3/13 Constant-pressure MC, Periodic Boundaries  
12 Tue 3/25 Analysis of Results, Gibbs Ensemble MC  
13 Thu 3/27 Molecular Dynamics; Hyperchem MD Ch. 10
14 Tue 4/1 Constant-temperature MD, measuring diffusion # 4
15 Thu 4/3 Quantum Modeling Ch. 11,13  
16 Tue 4/8 Quantum Modeling (cont.) and Na example Ch. 14  
Thu 4/10 No class Ch. 15,16
17 Tue 4/15 Hartree-Fock approach # 5
18 Thu 4/17 Hartree-Fock approach (cont.) and examples Ch. 17  
19 Tue 4/22 Semi-empirical methods (example) and Correlations Ch. 18,19  
20 Thu 4/24 Free Energies
21 Tue 4/29 Crystal Structures # 6
22 Thu 5/1 Multiscale methods, Dissipative Particle Dynamics (m1, m2, m3, m4) Ch. 24 Project definition
Tue 5/13 Dean's Day Project