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 (EQuad).

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 by email.

Staff: Prof. Thanos Panagiotopoulos, A317 EQuad., x8-4591 (azp@princeton). Office hour: Wed. 3-4 pm.
AI: Joey Vella, G107 EQuad, x8-0206 (vella@princeton) Office hours: Mon. and Thu. 3-4 pm.

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

Tentative Course Syllabus: 2/10/2016

Lec.#

Date

Topic(s)

Reading Assignment
1 Tue 2/2 Introduction and Intermolecular Forces Ch. 1  
2 Thu 2/4 Intermolecular Forces (cont.) Ch. 2  
3 Tue 2/9 Molecular Mechanics Ch. 3,4
4 Thu 2/11 Energy Minimization, Intro to Hyperchem Ch. 5,6
5 Tue 2/16 Conformational Search, Sampling from Probability Distributions Ch. 6,7 # 1
6 Thu 2/18 Matlab Programming and examples Files: 1, 2  
7 Tue 2/23 Statistical Mechanical Ensembles Ch. 8, Notes  
Thu 2/25 Statistical Mechanical Ensembles (cont.) Notes # 2
8 Tue 3/1 Monte Carlo Ch. 9
9 Thu 3/3 TBA  
10 Tue 3/8 Grand Canonical MC # 3
11 Thu 3/10 Constant-pressure MC, Periodic Boundaries  
12 Tue 3/22 Analysis of Results, Gibbs Ensemble MC  
13 Thu 3/24 Molecular Dynamics; Hyperchem MD Ch. 10
14 Tue 3/29 Constant-temperature MD, measuring diffusion # 4
15 Thu 3/31 Quantum Modeling Ch. 11,13  
16 Tue 4/5 Quantum Modeling (cont.) and Na example Ch. 14  
Thu 4/7 TBA
17 Tue 4/12 Hartree-Fock approach Ch. 15,16 # 5
18 Thu 4/14 Hartree-Fock approach (cont.) and examples Ch. 17  
19 Tue 4/19 Semi-empirical methods (example) and Correlations Ch. 18,19  
20 Thu 4/21 Free Energies
21 Tue 4/26 Crystal Structures # 6
22 Thu 4/28 Multiscale methods, Dissipative Particle Dynamics (m1, m2, m3, m4) Ch. 24 Project definition
Tue 5/10 Dean's Day Project