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Cell Lists
Cell lists (also sometimes referred to as cell linked-lists) is a data structure in molecular dynamics simulations to find all atom pairs within a given cut-off distance of each other. These pairs are needed to compute the short-range non-bonded interactions in a system, such as Van der Waals forces or the short-range part of the electrostatic interaction when using Ewald summation. Algorithm Cell lists work by subdividing the simulation domain into cells with an edge length greater than or equal to the cut-off radius of the interaction to be computed. The particles are sorted into these cells and the interactions are computed between particles in the same or neighbouring cells. In its most basic form, the non-bonded interactions for a cut-off distance r_c are computed as follows: :for all neighbouring cell pairs (C_\alpha, C_\beta) do ::for all p_\alpha \in C_\alpha do :::for all p_\beta \in C_\beta do ::::r^2 = \, \mathbf x _\alpha- \mathbf x _\beta\, _2^2 ::::if r^2 \le r_c^2 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. 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. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Van Der Waals Force
In molecular physics, the van der Waals force is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and therefore more susceptible to disturbance. The van der Waals force quickly vanishes at longer distances between interacting molecules. Named after Dutch physicist Johannes Diderik van der Waals, the van der Waals force plays a fundamental role in fields as diverse as supramolecular chemistry, structural biology, polymer science, nanotechnology, surface science, and condensed matter physics. It also underlies many properties of organic compounds and molecular solids, including their solubility in polar and non-polar media. If no other force is present, the distance between atoms at which the force becomes repulsive rather than attractive as the atoms approach one another is called the van der Waals contact distance; this phenomenon resul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ewald Summation
Ewald summation, named after Paul Peter Ewald, is a method for computing long-range interactions (e.g. electrostatic interactions) in periodic systems. It was first developed as the method for calculating electrostatic energies of ionic crystals, and is now commonly used for calculating long-range interactions in computational chemistry. Ewald summation is a special case of the Poisson summation formula, replacing the summation of interaction energies in real space with an equivalent summation in Fourier space. In this method, the long-range interaction is divided into two parts: a short-range contribution, and a long-range contribution which does not have a singularity. The short-range contribution is calculated in real space, whereas the long-range contribution is calculated using a Fourier transform. The advantage of this method is the rapid convergence of the energy compared with that of a direct summation. This means that the method has high accuracy and reasonable speed when co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Periodic Boundary Conditions
Periodic boundary conditions (PBCs) are a set of boundary conditions which are often chosen for approximating a large (infinite) system by using a small part called a ''unit cell''. PBCs are often used in computer simulations and mathematical models. The topology of two-dimensional PBC is equal to that of a ''world map'' of some video games; the geometry of the unit cell satisfies perfect two-dimensional tiling, and when an object passes through one side of the unit cell, it re-appears on the opposite side with the same velocity. In topological terms, the space made by two-dimensional PBCs can be thought of as being mapped onto a torus (compactification). The large systems approximated by PBCs consist of an infinite number of unit cells. In computer simulations, one of these is the original simulation box, and others are copies called ''images''. During the simulation, only the properties of the original simulation box need to be recorded and propagated. The ''minimum-image conventi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Verlet List
A Verlet list (named after Loup Verlet) is a data structure in molecular dynamics simulations to efficiently maintain a list of all particles within a given cut-off distance of each other. This method may easily be applied to Monte Carlo simulations. For short-range interactions, a cut-off radius is typically used, beyond which particle interactions are considered "close enough" to zero to be safely ignored. For each particle, a Verlet list is constructed that lists all other particles within the potential cut-off distance, plus some extra distance so that the list may be used for several consecutive Monte Carlo "sweeps" (set of Monte Carlo steps or moves) before being updated. If we wish to use the same Verlet list n times before updating, then the cut-off distance for inclusion in the Verlet list should be R_c + 2nd, where R_c is the cut-off distance of the potential, and d is the maximum Monte Carlo step (move) of a single particle. Thus, we will spend of order N^2 time to compute ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. 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. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials. Examples of such properties are structure (i.e., the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments, vi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Physics
Molecular physics is the study of the physical properties of molecules and molecular dynamics. The field overlaps significantly with physical chemistry, chemical physics, and quantum chemistry. It is often considered as a sub-field of atomic, molecular, and optical physics. Research groups studying molecular physics are typically designated as one of these other fields. Molecular physics addresses phenomena due to both molecular structure and individual atomic processes within molecules. Like atomic physics, it relies on a combination of classical and quantum mechanics to describe interactions between electromagnetic radiation and matter. Experiments in the field often rely heavily on techniques borrowed from atomic physics, such as spectroscopy and scattering. Molecular Structure In a molecule, both the electrons and nuclei experience similar-scale forces from the Coulomb interaction. However, the nuclei remain at nearly fixed locations in the molecule while the electrons ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Physics
Computational physics is the study and implementation of numerical analysis to solve problems in physics for which a quantitative theory already exists. Historically, computational physics was the first application of modern computers in science, and is now a subset of computational science. It is sometimes regarded as a subdiscipline (or offshoot) of theoretical physics, but others consider it an intermediate branch between theoretical and experimental physics - an area of study which supplements both theory and experiment. Overview In physics, different theories based on mathematical models provide very precise predictions on how systems behave. Unfortunately, it is often the case that solving the mathematical model for a particular system in order to produce a useful prediction is not feasible. This can occur, for instance, when the solution does not have a closed-form expression, or is too complicated. In such cases, numerical approximations are required. Computational phys ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
