Types of Molecular Dynamics Simulation

Molecular dynamics is a powerful technique that uses approximations of known laws of physics to predict and analyze the motions of simulated atoms. The technique has been used to probe the function and action of many biological molecules, allowing researchers to test hypothesis to an unprecedented resolution. There are many types of molecular dynamics simulations, each designed to give a certain balance of accuracy and speed to answer very specific questions.

1) Traditional molecular mechanics. In these systems, Newtonian physics is used to create the motion of atoms, using empirically derived potentials to describe attributes such as bonds, angles, torsions, dihedrals, van der Waals radii, and electrostatics. These potentials are called “force fields”. The main computational expense with traditional MM comes with the non-bonded interactions, specifically the van der Waals and electrostatics. These interactions involve every pairwise combination of particles, as opposed to interactions such as bonds which only involve neighboring atoms.

Traditional molecular mechanics represents all bonded interactions as simple harmonic springs. While this makes the calculation cheap and simple, it removes the ability to break bonds. This limits the applications of molecular mechanics to general system dynamics and movement, rather than simulating chemical reactions.

2) Semi-empirical. These take advantage of the accuracy of quantum mechanics to make molecular dynamics more powerful. Matrix representations from quantum mechanics are used to determine energy contributions from electron orbitals and then utilize these energies to move the system.

3) Polarizable. Induced dipoles, introduced through various means including fluctuating charges, allow for particles to change as the environment around the particles change. The future of field appears to be in polarizable MD simulations, as they have been shown, in general, to more accurately represent true physical systems.

4) Quantum mechanics/molecular mechanics (QM/MM). One weakness of molecular mechanics is the fact that because bonds are represented as simple springs, it is impossible for bonds to form or break. By representing a region of the simulation space with quantum mechanics, you remove this limitation while still using some molecular mechanics throughout the system to maintain a higher speed. Despite this hybrid nature, QM/MM is generally far more computationally expensive than traditional molecular mechanics.

5) Coarse-graining. While many of the types listed above try to include more information to make molecular dynamics more realistic, coarse-graining removes some of the accuracy to speed up the calculations. In coarse-graining, some sort of vast approximation is made to greatly increase simulation speed. For instance, some united atom methods represent groups of atoms with one large pseudo-atom that attempts to represent the overall properties of the represented atoms.