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 mechanics force fields. The method is applied mostly in chemical physics, materials science, and the biophysics.
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.
A solvation shell is the solvent interface of any chemical compound or biomolecule that constitutes the solute. When the solvent is water it is often referred to as a hydration shell or hydration sphere. The number of solvent molecules surrounding each unit of solute is called the hydration number of the solute.
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
An ionic liquid (IL) is a salt in the liquid state. In some contexts, the term has been restricted to salts whose melting point is below some arbitrary temperature, such as 100 °C (212 °F). While ordinary liquids such as water and gasoline are predominantly made of electrically neutral molecules, ionic liquids are largely made of ions and short-lived ion pairs. These substances are variously called liquid electrolytes, ionic melts, ionic fluids, fused salts, liquid salts, or ionic glasses.
Deep eutectic solvents are systems formed from a eutectic mixture of Lewis or Brønsted acids and bases which can contain a variety of anionic and/or cationic species. They are classified as types of ionic solvents with special properties. They incorporate one or more compound in a mixture form, to give a eutectic with a melting point much lower than either of the individual components. One of the most significant deep eutectic phenomenon was observed for a mixture of choline chloride and urea in a 1:2 mole ratio. The resulting mixture has a melting point of 12 °C, which makes it liquid at room temperature.
In the context of molecular modelling, a 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 and molecular dynamics simulations. The parameters of the energy functions may be derived from experiments in physics or chemistry, calculations in quantum mechanics, or both.
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
Free energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations.
A collision cascade is a set of nearby adjacent energetic collisions of atoms induced by an energetic particle in a solid or liquid.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
This is a list of computer programs that are used for nucleic acids simulations.
Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit or in implicit water models. Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field.
Biochemical and Organic Simulation System (BOSS) is a general-purpose molecular modeling program that performs molecular mechanics calculations, Metropolis Monte Carlo statistical mechanics simulations, and semiempirical Austin Model 1 (AM1), PM3, and PDDG/PM3 quantum mechanics calculations. The molecular mechanics calculations cover energy minimizations, normal mode analysis and conformational searching with the Optimized Potentials for Liquid Simulations (OPLS) force fields. BOSS is developed by Prof. William L. Jorgensen at Yale University, and distributed commercially by Cemcomco, LLC and Schrödinger, Inc.
Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2).
MacroModel is a computer program for molecular modelling of organic compounds and biopolymers. It features various chemistry force fields, plus energy minimizing algorithms, to predict geometry and relative conformational energies of molecules. MacroModel is maintained by Schrödinger, LLC.
Martini is a coarse-grained (CG) force field developed by Marrink and coworkers at the University of Groningen, initially developed in 2004 for molecular dynamics simulation of lipids, later (2007) extended to various other molecules. The force field applies a mapping of four heavy atoms to one CG interaction site and is parametrized with the aim of reproducing thermodynamic properties.
Spontelectrics is a form of solid state thin films with some peculiar physical properties.
The circuit topology of a linear polymer refers to arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. For defining the circuit topology, contacts are defined depending on the context. For proteins with disulfide bonds, these bonds could be considered as contacts. In a context where beta-beta interactions in proteins are more relevant, these interactions are used to define the circuit topology. As such, circuit topology framework can be applied to a wide range of applications including protein folding and analysis of genome architecture. In particular, data from Hi-C and related technologies can be readily analysed using circuit topology framework.
Klaas Wynne is a Professor in the School of Chemistry at the University of Glasgow and chair of Chemical Physics. He was previously a professor in the Department of Physics at the University of Strathclyde (1996–2010). He received his BSc in Chemistry from the University of Amsterdam in 1987 and his PhD in Chemistry from the University of Amsterdam in 1990 under the supervision of Joop van Voorst. He did his postdoctoral fellowship in the laboratory of Robin Hochstrasser at the University of Pennsylvania.
