Molecular Dynamics Simulations of Simple Liquids

Abstract

Students perform molecular dynamics simulations on a simple molecular liquid using the Amber suite of programs. They are introduced both to the physical theories underlying classical mechanics simulations and to the atom–atom pair distribution function. Using this distribution function, the students can graphically "see" that liquids do, in fact, possess long-range microscopic structure and that the extent of this structure differs from liquid to liquid and from one temperature to another. Students are given the coordinate and potential information for four chemically different liquids: water, benzene, ethanol, and acetonitrile. In the spirit of the inquiry-based approach, each group of students is asked to design a set of simulations to answer a self-determined question. This gives the students an opportunity to develop their own scientific creativity. For example, students have designed experiments that range from examining the effect of temperature on the long-range microscopic structure of a single liquid, such as ethanol, to exploring how much the hydrogen bonding structure of water differs from that of ethanol. Students are also shown how to view ball-and-stick and close-packed pictures of their simulated liquids.