Molecular Simulation

Molecular Dynamics is a method to perform Molecular Simulation research.

Aim: Generate enough representative confirmations of the molecular system in such a way that accurate values of a property can be obtained.

Example:

Protein ion channel in a lipid bi-layer

Typical questions:

• How fast do ions pass through channels?

• What happens when protein residues are altered?

• How and where do ligands bind to the channel?

• How is the lipid bi-layer composed locally?

One Method: Molecular Dynamics

Molecular Dynamics

Uses Newton’s equations of motion to generate configurations (a trajectory) for atoms of a molecular system.

\( m\frac{d^2x}{dt^2} = F \)

\( F = - \nabla U \)

These are integrated using a Verlet-Like integrator, the Velocity-Verlet formulation is

GROMACS

GROMACS is a command line MD package that can perform most aspects of a MD workflow.