Module 4: Molecular simulations and Thermodynamics

Module 4: Molecular simulations and Thermodynamics#

The sections included here are

  1. Introduction to Molecular Dynamics

    1. For non-ideal gases, the partition function is not analytical

    2. First step of molecular dynamics: initial position of your particles

    3. Second step: calculate the potential energy

    4. Third step: give velocity to particles for thermal distribution

    5. Solve equations of motion step by step: run a simple molecular dynamics

  2. Introduction to molecular simulations

    1. Identifying the main charactersitics of molecular simulations

    2. Running a molecular dynamics simulation of water

    3. Analyzing a molecular dynamics simulation of water

  3. Calculating free energies of molecular systems

    1. Free energies as a function of a geometric parameter

    2. Free energy of rotation of ethane

    3. The free energy along the dihedral angle of butane