PhD course in Simulation Methods in Many-Particle Systems
Autumn 2018


Book: Frenkel and Smit: Understanding Molecular Simulations, available electronically from the library website.

Lecturer and course responsible: Astrid de Wijn.


The examination consists of a theory part (hand-in exercises and oral exam) and a practical part, programming assignments. You must pass everything to pass the course. Some addition notes:


Schedule and preliminary plan for lectures. This may change as we go along.

Lecture date/time/location topic(s) reading material assignments to be handed in
1 2 Fri. 28 Sept. 9:00 - 12:00, 250B What and why. Introduction into MD and MC. Structure of a simulation. Practical issues with programming. Lennard-Jones potential. Chapter 1, sections 4.1, 4.2.1, 4.2.2. none
2 3 Fri. 19 Oct. 9:00 - 12:00, 250B Integration algorithms: Verlet and Runge-Kutta. Symplectic integration. 4.2.3, 4.3, A.3.2 programming 1.1
4 Fri. 26 Oct. 9:00 - 12:00, 250B Resource scaling, Lyapunov instability, cutoffs. Ewald summation. 4.3 programming 1.2 and 1.3, hand-in 1
5 6 Fri. 2 Nov. 9:00 - 12:00, 250B Ewald summation. Statistical physics! Ensembles. Averages. 12.1 A.3.3, D.3 programming 1.4, hand-in 2 and 3
7 8 Wed. 7 Nov. 9:00 - 12:00, 250B Thermostats, Langevin and Nosé-Hoover. Radial distribution function. Langevin and Nosé-Hoover. Introduction into MC, MC integration. Importance sampling, Ising model as an example. 6.1, 6.2 3.1, 3.2, 5.1, 5.2 programming 1.5 and 1.6, hand-in 4
8 9 Fri. 9 Nov. 9:00 - 12:00, 250B Markov chains. Detailed balance. Metropolis. Trial moves, early rejection. Cluster moves. Ensembles in MC. 3.3, 5.3, 5.4, 14.3 programming 1.7 and 1.8, hand-in 5
10 11 Fri. 16 Nov. 9:00 - 12:00, 250B Free-energy calculations. Effective force fields, internal degrees of freedom of molecules. 7.1, 7.2, (7.3, 7.4) programming 1.9 and 1.10, hand-in 6
11 12 Fri. 23 Nov. 9:00 - 12:00, 250B Constraints, SHAKE. Quantum MD, Car-Parrinello, diffusion quantum MC, if there is time. 15.1, 15.2 programming 1.11, hand-in 7 and 8
Fri. 30 Nov. 9:00 - 12:00, 250B Buffer time. Everything! programming 2.1 and 2.2
Fri. 7 Dec. 9:00 - 12:00, Astrid's office Oral exams Everything!