Tutorial 1_LJ2

Tutorial 1_LJ2 - Oscar Tutorial 1 page 1 Tutorial 1 Two...

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Oscar Tutorial 1 page 1 Tutorial 1: Two Atoms of Lennard-Jonesium Download the file LJ2.pdb. This contains the coordinates of two atoms that interact through the Lennard-Jones 6-12 potential. A collection of such atoms is often called “Lennard-Jonesium.” Predictions Read the coordinates of the two atoms from the PDB file. You will see that they are both positioned on the x- axis. What is the distance between the two atoms? Now let’s try to predict the behavior of the system. You are going to run a free MD simulation, which means that the intial velocities of both atoms are zero. Feel free to discuss your predictions with other students before you make final predictions. You will receive points for turning in predictions. You will not be marked down for wrong predictions! What do you predict will happen during the first few steps of MD? Describe the predicted behavior in words. Also make sketches of what you predict plots will look like for d(t) [the interatomic distance as a function of time], PE(t), KE(t) and E tot (t) over the first few time steps. Label the axes in your plots, but don’t attempt to estimate numbers unless you think you can do so with confidence.

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