Briefly, Molecular Dynamics#

The general steps of molecular dynamics (MD) simulations are shown below, consider the following questions for each step:

System Preparations
- What ions or molecules are in your system?
- Is the force field for each type of ion/molecule sufficient?
- What protonation states are your titratable residues?
Equilibrate the System
- What is the target environmental conditions for your system?
- Is temperature, pressure, and/or the energy of the system stable?
Production Simulations
- How long do you need your simulation?
Analysis of Trajectories
- What property of the system addresses your hypothesis?

Classical Mechanics#

Molecular dynamic (MD) simulations use classical Newtonian mechanics to describe the motions of atoms and molecules.

These simulations involve:

Explicit a particles (atoms, ions)
Particles interact via relatively simple analytical potential (i.e. force field)
Newton’s equations of motion are integrated for all particles simultaneously
Hundreds to millions of particles depending on model
Simulation time could be from 10 ps to 1 μs depending on model (typically nanosecond)

Energy is:

\[ E_{total} = E_{bonded} + E_{nonbonded} \]

The bonded and nonbonded terms are:

\[ E_{total} = E_{bonds} + E_{angles} + E_{torsion} + E_{vDW} + E_{Coulomb} \]

and each energy contribution term has a potential function, for example, the van der waals term \(E_{vDW}\) is defined by the Lennard-Jones potential:

\[ E_{vDW} = 4\epsilon \left[ (\frac{\sigma}{r})^{12} - (\frac{\sigma}{r})^{6} \right] \]

The potential functions have preset bonding arrangements, therefore, classical MD on its own cannot be used to model chemical reactions.

MD simulation generates a sequence of configurations phase space connected by time. This is called a trajectory of all particles in the system as a function of time. Time averages and other properties can be calculated from a trajectory.