Molecular dynamics

We consider molecular dynamics (MD) as an approach to obtain:

1. Thermodynamic properties (energy, heat capacity etc.)

2. Dynamic information (diffusion coefficient, dielectric functions, correlated motion etc.)

MD is a classical approach based on Newton’s equations of motion. Each atom in a structure is assigned parameters that describe both bonding and non-bonding interactions. The parameters are shown graphically below. The potential energy of the system is given by these terms. The kinetic energy is given in the form of a Maxwell-Boltzmann distribution of velocities.

In order to propagate a molecular system using a force field there are three typical stages.

1. Minimization

2. Equilibration

3. Dynamics

Figure 1. Graphical representation of the terms that contribute to a force field.

Figure 2. Mathematical form of terms that contribute to a force field.

For macromolecules (peptides, oligonucleotides, and oligosaccharides) the conformations can involve many different possible states of nearly the same energy. The interconversion involves thermal motion. Crossing from one conformation to another involves transit over a barrier. If k_BT is greater than the barrier height then this will occur with high probability. If k_BT is less than the barrier height the system will be confined to a smaller region of conformational space.

Figure 3. Graphical representation of the relative magnitude of thermal energy and energy barriers in the force field.