Molecular Dynamics

Abstract

Molecular dynamics (MD) is a handy computer simulation method which unveils principles of a large variety of fundamental processes by mimicking the real life perpetual motion of atoms triggered by interatomic forces. In MD, these forces are expressed through analytical functions and associated parameters, which are commonly referred to as the force field. The forces' effect on the movement of atoms is determined by Newton's second law. Most importantly, MD simulations are able to retrace the exact trajectories of interacting atoms by following their spatial evolution in time from a defined initial configuration. The resulting integrated trajectory of the system can be visualised and analysed with rigorous mathematical expressions of statistical mechanics, which relate averaged microscopic states to macroscopic properties relevant to the problem at hand. Key Concepts Molecular dynamics is a computation tool successfully used to unveil principles of a large variety of fundamental processes down to the atomic resolution. Thanks to recent advances in computer simulations, atomistic MD can reach millisecond timescales, thus emerging as a powerful alternative method that successfully complements experimental measurements in biology. Computational efficiency of molecular dynamics algorithms continues to pose challenges. The collective efforts of many groups of researchers have enabled a great deal of force fields applied to many problems in biology. Biomolecular simulations require the presence of solvent; hence, a reliable representation of water is crucial for achieving realistic results. Several specialised methods stemming from MD allow to investigate various processes of biomolecules: REMD, SMD and TMD.

Computational Studies of Cellulose-based Materials

“…Molecular Dynamics (MD) is a pivotal computational methodology enabling simulations of molecules and material behavior at nanoscale under various conditions, such as in solutions, at interfaces, or at specific temperatures and pressures 54,55 . This method has many practical applications in various fields, including physical chemistry, material science, molecular biology, etc [54][55][56] . Importantly, MD simulations can track the spatial dynamics of atoms to record the precise trajectories of molecules.…”

Role of crystallographic orientation in material behaviour under nanoindentation: Molecular Dynamics study

“…Molecular dynamics [11][12][13] is a powerful tool for evaluating materials' behaviour and predicting their properties. MD is a well-established research tool in various fields, e.g., biology [14], chemistry [15], physics [16], and also materials science [17].…”