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Molecular modelling [M12]

During this course, students will develop an understanding of the atomic scale processes behind familiar macroscopic concepts like temperature and stress/strain curves, and learn how to compute and predict various observables. A few introductory lectures are given to introduce atomistic simulation and the associated software tools, but most of the course consists of completing the simulation and programming assignments. Students can get help from the course leader and/or demonstrators in the DPO in the time slots advertised for the course. The assignments and the necessary data files are available from the associated CamTools support site.

Topics

Harmonic oscillators

Students are introduced to the concepts of molecular dynamics via the simplest possible system, the harmonic oscillator. Everyone develops their own program from scratch to simulate the behaviour of a series of increasingly more complicated systems, ending up with a system of particles connected by springs - an elementary model of a solid. Connections are made between the microscopic quantities derived from atomic trajectories and macroscopic observables such as temperature, thermal expansion and phonon relaxation processes.

Structure of water

The students create a representation of a small "box" of water molecules on which molecular dynamics is performed using a standard package (NAMD). Analysis programs are written by students to evaluate the following observables concerning the structure and dynamics of water: O-O pair correlation function, molecular diffusivity, O-H distance and O-H..O angular distribution functions.

Elastic properties of proteins

Students receive a file containing the atomic positions of a polypeptide. This is placed in a box of water molecules. After equilibrating, the box is stretched, while holding the ends of the molecule with a fixed force and the average strain is measured. From several data points, the Young's Modulus can be calculated. The assignment introduces the concepts of measurement and statistical noise in molecular simulation.

 

References

Recommended background reading: D. Frenkel, B. Smit: Understanding Molecular Simulation