This interface is a boundary where a polar aqueous phase and a hydrophobic non-polar phase meet. In MD Newton's equations of motion are solved given an emperically based force field. MD allows us to view how the molecular system evolves through time and to constuct average properties of the system given a long enough simulation.
Minimization includes first defining the force field parameters for the atoms.
The parameters include force constants for bond stretching, bond bending and torsional rotation. Electrostatic interactions are generally just point charges located at the center of the atom that are calculated by Coulomb's law. The minimization occurs usually by second derivative methods in order to reduce the gradient of force on all atoms to an acceptable level. Then the molecular dynamics is carried out by first heating the system to the experimental temperature by scaling of the velocities. How the system evolves through time is specified by the force field and an integration time step that determines where the atoms should be at a later time.