MSE 504 / CHM 560 / PHY 512 / CBE 520: Monte Carlo and Molecular Dynamics Simulations – Spring 2013


Course organization


Lectures are on Mondays and Wednesdays from 10:30–11:50 am, in Comp. Sci. Rm 102. Makeup lectures are on Fridays, 10:30–11:50 am, in EQuad Room E225.


There will be 5 programming assignments (60% of the grade) and a final project (30%) – class participation contributes 10%.  Assignments require access to a C or FORTRAN compiler (see this link on how to access Princeton's Unix systems).


We will be using the textbook by D. Frenkel and B. Smit, "Understanding Molecular Simulation," 2nd Ed., Academic Press, London, 2002.


 Tentative course syllabus (detailed schedule)


1. Introduction

           Scope of molecular simulation, computer hardware

            Classical potential functions

            Statistical mechanical ensembles

            Elements of modern Fortran programming

2. Simple Monte Carlo methods

            Random numbers and random distributions

            Importance Sampling, Metropolis and Barker acceptance

            Canonical Ensemble MC

            Constant-pressure and Grand Canonical MC

3. Simple Molecular Dynamics methods

            Equations of motion

            Time correlation functions

            Calculation of transport properties

            Extended Hamiltonian methods

4. Free energies and phase equilibria

            Histogram reweighting, flat histogram methods

            Thermodynamic Integration

            Widom Test Particles

            Non-equilibrium work theorem

            The Gibbs Ensemble

            Determination of critical points / finite-size scaling

            Solid free energies and Gibbs-Duhem integration

            Polymers: Configurational-bias sampling

5. Special Topics

            Dynamic Monte Carlo

            Transition path and transition interface sampling

            Infinite-range forces and Ewald sums