In this first part of the course you have learned;

You have also been introduced to two different Monte Carlo moves;

  1. Random translation of atoms. A random atom is randomly translated, with the change in energy accepted using the NVT or NPT acceptance test.
  2. Random changes in volume. The volume of the periodic box is randomly changed, with all atoms in the box scaled from the box center. The change in energy and change in volume are used to accept the move using the NPT acceptance test.

You have also seen that Monte Carlo moves are individually fast (thousands of moves per second using the C++ program), but that you need to run millions of moves to equilibrate the energy and volume occupied by the molecules.

While all of the above was demonstrated using a box of krypton atoms, it is equally true when applied to simulations of biomolecules. To learn how to perform Monte Carlo simulations of biomolecules, please proceed to part 2 of the course.

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