Description and contextualization of the subject

Provide students with knowledge and abilities to generate accurate and stable atomistic dynamical trajectories of nanoscale systems, and at the same time, convince them that molecular dynamics simulations are also and foremost about understanding the statistical properties of these trajectories.

Temary

1. Computer Simulations

2. Molecular Dynamics (MD) Simulations

3. A MD Program

a) Reduced Units

b) Truncating Interactions

c) Initialization

d) The Force Calculation

e) The propagation of the Dynamics

4. MD algorithms

a) Speed

b) Accurate for large time steps

c) Memory

d) Energy Conservation

e) Accuracy

f) Reversibility

5. Liouville Formulation of Time-Reversible Algorithms

6. Computer Experiments

a) Diffusion

7. Linear Response Theory

a) Static Response

b) Dynamic Response

c) Dissipation

8. Constraints

a) Lagrangian Formulation

b) Constrained and Unconstrained Averages

9. Rare Events

10. Molecular Dynamics in Various Ensembles. Non-Hamiltonian Dynamics.

a) Molecular Dynamics at Constant Temperature

b) The Andersen Thermostat

c) The Nose-Hoover Thermostat

d) Molecular Dynamics at Constant Pressure

11. Ab Initio Molecular Dynamics

a) Born-Oppenheimer Molecular Dynamics

b) Car-Parrinello Molecular Dynamics

Bibliography

Basic bibliography

D. Frenkel, B. Smit. Understanding Molecular Simulations, Academic Press, London, 2002.



Michael P. Allen, Introduction to Molecular Dynamics Simulation. In: “Computational Soft Matter: From Synthetic Polymers to Proteins”, Lecture Notes, Norbert Attig, Kurt Binder, Helmut Grubmuller, Kurt Kremer (Eds.). John von Neumann Institute for Computing, Julich, NIC Series, Vol. 23, 2004.



D. Chandler, Introduction to Modern Statistical Mechanics, Oxford University Press, New York, 1987.