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Tutorial_2_LJ10_MD - Oscar Tutorial 2 page 1 Tutorial 2...

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Oscar Tutorial 2 page 1 Tutorial 2: Ideal Gas in a Two-Dimensional Box Download the files LJ10.pdb and LJ10x.pdb. Each of these contains the coordinates of ten atoms that interact through the Lennard-Jones 6-12 potential. Ideal Gas in a Box In this exercise you will use Oscar to simulate ten atoms of an ideal gas. 1. Start Oscar and run a molecular dynamics simulation with the following settings: Coordinate File LJ10.pdb Structure File (none) Output Folder (choose one by browsing) Job Name LJ10_MD_free Output Interval 100 steps (default) Raw Coordinates Off --- Algorithm Molecular Dynamics --- Time Step 0.001 ps (default) Number of Steps 100,000 (default) Initial Temperature 0.0 K Box Side Length 20 Å Number of Dimensions 2 Initial Seed (leave blank) --- Thermalization Method Off Once started, the simulation should take less than a minute to run. Make a plot of potential energy, kinetic energy, and total energy as a function of time. Explain what is happening during the first 2000 steps. Watch the trajectory in VMD.
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Oscar Tutorial 2 page 2 2. Repeat the previous simulation, but this time set the initial temperature to 300.0
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