"Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules."
A method used to study the behavior of a system of interacting particles over time.
Statistical mechanics: The study of the behavior of systems made up of large numbers of interacting particles using statistical methods.
Thermodynamics: The study of the relationships between heat, work, and energy in systems, including the properties of matter and the phase transitions.
Kinetic theory: The study of the motion of particles in a system, including the velocity distribution and pressure.
Hamiltonian mechanics: The study of the motion of particles in a system using the Lagrangian (energy function) and the equations of motion developed by William Hamilton.
Classical mechanics: The study of the motion of objects in a system using Newton’s laws of motion, energy, and momentum conservation.
Molecular dynamics simulation: The use of computer algorithms to simulate the generated motion of atoms and molecules over time, as dictated by the relevant equations of motion.
Force fields: Mathematical descriptions of the interactions between atoms and molecules that are used to simulate the dynamics of a system in a molecular dynamics simulation.
Integrators: Algorithms designed to numerically solve the equations of motion in molecular dynamics simulations.
Ensemble-based methods: Statistical methods used to extract physical properties of the system from molecular dynamics simulations.
Conformational analysis: The study of the conformations and structural transitions of molecules and proteins.
Coarse-grained models: Models that simplify the representation of the interactions between particles to improve computational performance while still providing an accurate description of the system.
Steered molecular dynamics: A specialized form of molecular dynamics simulation used to study the motion of molecular systems under externally applied forces.
Classical Molecular Dynamics Simulation: This type of simulation uses classical mechanics to describe molecular behavior, specifically the motion of atoms, molecules, and their interactions in a system. It calculates the position, velocity, and acceleration of each particle over time.
Quantum Molecular Dynamics Simulation: This type of simulation uses quantum mechanics to describe the behavior of molecules or atoms in a system. Unlike classical simulations, quantum simulations take into account the wave-like behavior of particles, which is important in describing certain reactions and properties.
Coarse-Grain Molecular Dynamics Simulation: This type of simulation simplifies the molecular system by grouping atoms or molecules into larger units. This reduces computational complexity while still being able to capture essential features of the system.
Accelerated Molecular Dynamics Simulation: This type of simulation speeds up the simulation process by applying external forces to the system, which helps to overcome energy barriers and allows the system to explore a wider range of conformational space.
Replica Exchange Molecular Dynamics Simulation: This type of simulation uses multiple replicas of the same system at different temperatures to speed up sampling of the conformational space.
Ab Initio Molecular Dynamics Simulation: This type of simulation employs quantum mechanical calculations to determine the electronic structure and force field of the system in real-time. The simulation enables the description of bond breaking, bond formation, and reaction pathways.
Free-Energy Perturbation Molecular Dynamics Simulation: This type of simulation calculates the free-energy difference between two states of a system. It is typically used to investigate binding or conformational changes in biomolecules such as proteins and nucleic acids.
Steered Molecular Dynamics Simulation: This type of simulation applies an external force to a molecule or atom in a particular direction to drive the system towards a specific conformation or reaction pathway.
Metadynamics Simulation: This type of simulation uses external potential energy to explore free energy landscapes in complex systems such as proteins or nucleic acids.
Implicit Solvent Molecular Dynamics Simulation: This type of simulation considers the effect of a solvent implicitly using a simplified representation that takes into account its average properties. This is often useful when computational resources are limited.
Hybrid Molecular Dynamics Simulation: This type of simulation combines the strengths of two or more types of simulations, such as classical and quantum mechanics, to model complex biochemical systems.
"The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic 'evolution' of the system."
"The trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles."
"Forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields."
"The method is applied mostly in chemical physics, materials science, and biophysics."
"Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods."
"Long MD simulations are mathematically ill-conditioned, generating cumulative errors in numerical integration."
"The cumulative errors in numerical integration can be minimized with proper selection of algorithms and parameters, but not eliminated."
"For systems that obey the ergodic hypothesis, the evolution of one molecular dynamics simulation may be used to determine the macroscopic thermodynamic properties of the system."
"The time averages of an ergodic system correspond to microcanonical ensemble averages."
"MD has also been termed 'statistical mechanics by numbers'."
"MD [provides] insight into molecular motion on an atomic scale."
"The objective of MD simulations is to observe the physical movements and interactions of atoms and molecules."
"MD simulation circumvents [the problem of determining complex system properties] by using numerical methods."
"MD is applied in chemical physics, materials science, and biophysics to gain insights into molecular behavior."
"Trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion."
"Cumulative errors in numerical integration can be minimized with proper selection of algorithms and parameters."
"MD simulation allows atoms and molecules to interact for a fixed period of time."
"Forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields."
"MD is primarily applied in chemical physics, materials science, and biophysics."