Tutorial_3_LJ10_min

Tutorial_3_LJ10_min - Oscar Tutorial 3 page 1 Tutorial 3:...

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Oscar Tutorial 3 page 1 Tutorial 3: Energy Minimization Minimization Algorithms In this exercise you will use Oscar to minimize ten atoms of an ideal gas (“Lennard- Jonesium” in two dimensions. You will need the file LJ10.pdb, which contains the coordinates of ten atoms that interact through the Lennard-Jones 6-12 potential. 1. Start Oscar and run a steepest descent minimization with the following settings: Coordinate File LJ10.pdb Structure File (none) Output Folder (choose one by browsing) Job Name LJ10_SD1 Output Interval 1 steps (get output at every step) Raw Coordinates Off --- Algorithm Energy Minimization --- Minimization Method Steepest Descent (default) Initial Step Size 0.0001 (default) Number of Steps 10000 (default) Convergence Criterion 0.00001 (default) --- Once started, the minimization should run to completion within a second or so. Make a plot of potential energy as a function of step number, and watch the trajectory in VMD. Explain what happens during the simulation. Did the minimization converge? Explain your answer.
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Oscar Tutorial 3 page 2 2. You will now repeat the previous simulation, but this time with a much tighter convergence criterion (10 -9 ) and a new output file name. Note: OSCAR will accept floating point numbers in either normal or exponential format. You can enter “10 -9 ” as either 0.000000001 or as 1e-9. To do this, just hit the “Back” button in OSCAR. You will be set up to run with all the same input value as in your first run. The only two changes you need to make are: Job Name LJ10_SD2 --- --- Convergence Criterion 1e-9 --- Again, plot the potential energy
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Tutorial_3_LJ10_min - Oscar Tutorial 3 page 1 Tutorial 3:...

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