Classical Molecular Dynamics Simulations

This lecture introduces classical force fields and molecular dynamics simulations, focusing on the propagation of atomic positions in time. It covers the ToyMD program, running molecular dynamics of CO2 gas, and the classical approximation to describe supramolecular properties. Topics include intramolecular and intermolecular interactions, the atomic force field, and sampling specific ensembles. The lecture also discusses the Lennard-Jones potential, force field parameterization, and the pair radial distribution function. Practical exercises involve running MD simulations in the NVT ensemble, investigating force fields, and visualizing radial distribution functions.

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Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.

Force field (chemistry)

In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.

Lorentz force

In physics (specifically in electromagnetism), the Lorentz force (or electromagnetic force) is the combination of electric and magnetic force on a point charge due to electromagnetic fields. A particle of charge q moving with a velocity v in an electric field E and a magnetic field B experiences a force (in SI units) of It says that the electromagnetic force on a charge q is a combination of a force in the direction of the electric field E proportional to the magnitude of the field and the quantity of charge, and a force at right angles to the magnetic field B and the velocity v of the charge, proportional to the magnitude of the field, the charge, and the velocity.

Comparison of force-field implementations

This is a table of notable computer programs implementing molecular mechanics force fields.

Interatomic potential

Interatomic potentials are mathematical functions to calculate the potential energy of a system of atoms with given positions in space. Interatomic potentials are widely used as the physical basis of molecular mechanics and molecular dynamics simulations in computational chemistry, computational physics and computational materials science to explain and predict materials properties.