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Oscar Tutorial 1
page 1
Tutorial 1:
Two Atoms of LennardJonesium
Download the file LJ2.pdb. This contains the coordinates of two atoms that interact
through the LennardJones 612 potential. A collection of such atoms is often called
“LennardJonesium.”
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.
If you run MD over a very long time, what do you predict will happen? Describe the
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This note was uploaded on 09/22/2011 for the course BIOL 7110 taught by Professor Steveharvey during the Spring '11 term at Georgia Institute of Technology.
 Spring '11
 SteveHarvey

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