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

Info icon This preview shows pages 1–2. Sign up to view the full content.

View Full Document Right Arrow Icon
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.
Image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Image of page 2
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern