Interpret the problem of time and length scales in molecular modeling by relating the type of the problem to the available modeling technique.
Sketch simple potential energy surfaces for systems of up to four particles and identify the global energy minimum and local energy minima on it.
Calculate the energy of conformations of simple molecules of up to six particles, given the parameters of a force field describing the molecule.
Relate the influence of conformations of a molecule on its properties by calculating the average properties of a given system based-on the Boltzmann distribution.
Perform conformational searching on systems of up to 10 particles by applying systematic and random search methods.
Perform normal mode analysis on systems of up to 10 particles in one and two-dimensions and relate the output to vibrational spectroscopy experiments.
Set-up and run molecular dynamics simulations on complex systems such as polymers and proteins.
Make physics-based descriptions of the main ingredients of a simulation such as the Verlet algorithm, periodic boundary conditions, selection of time step.
Calculate thermodynamic (e.g. temperature, pressure, heat capacity), and kinetic properties (diffusion constant, various relaxation times) from simulated trajectories.