Verlet integrationVerlet integration (vɛʁˈlɛ) is a numerical method used to integrate Newton's equations of motion. It is frequently used to calculate trajectories of particles in molecular dynamics simulations and computer graphics. The algorithm was first used in 1791 by Jean Baptiste Delambre and has been rediscovered many times since then, most recently by Loup Verlet in the 1960s for use in molecular dynamics. It was also used by P. H. Cowell and A. C. C.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
IntegralIn mathematics, an integral is the continuous analog of a sum, which is used to calculate areas, volumes, and their generalizations. Integration, the process of computing an integral, is one of the two fundamental operations of calculus, the other being differentiation. Integration started as a method to solve problems in mathematics and physics, such as finding the area under a curve, or determining displacement from velocity. Today integration is used in a wide variety of scientific fields.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
Molecular dynamicsMolecular 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.
Symplectic integratorIn mathematics, a symplectic integrator (SI) is a numerical integration scheme for Hamiltonian systems. Symplectic integrators form the subclass of geometric integrators which, by definition, are canonical transformations. They are widely used in nonlinear dynamics, molecular dynamics, discrete element methods, accelerator physics, plasma physics, quantum physics, and celestial mechanics. Symplectic integrators are designed for the numerical solution of Hamilton's equations, which read where denotes the position coordinates, the momentum coordinates, and is the Hamiltonian.
Leapfrog integrationIn numerical analysis, leapfrog integration is a method for numerically integrating differential equations of the form or equivalently of the form particularly in the case of a dynamical system of classical mechanics. The method is known by different names in different disciplines. In particular, it is similar to the velocity Verlet method, which is a variant of Verlet integration. Leapfrog integration is equivalent to updating positions and velocities at different interleaved time points, staggered in such a way that they "leapfrog" over each other.
VelocityVelocity is the speed and the direction of motion of an object. Velocity is a fundamental concept in kinematics, the branch of classical mechanics that describes the motion of bodies. Velocity is a physical vector quantity: both magnitude and direction are needed to define it. The scalar absolute value (magnitude) of velocity is called , being a coherent derived unit whose quantity is measured in the SI (metric system) as metres per second (m/s or m⋅s−1). For example, "5 metres per second" is a scalar, whereas "5 metres per second east" is a vector.
Taylor seriesIn mathematics, the Taylor series or Taylor expansion of a function is an infinite sum of terms that are expressed in terms of the function's derivatives at a single point. For most common functions, the function and the sum of its Taylor series are equal near this point. Taylor series are named after Brook Taylor, who introduced them in 1715. A Taylor series is also called a Maclaurin series when 0 is the point where the derivatives are considered, after Colin Maclaurin, who made extensive use of this special case of Taylor series in the mid-18th century.
Numerical integrationIn analysis, numerical integration comprises a broad family of algorithms for calculating the numerical value of a definite integral, and by extension, the term is also sometimes used to describe the numerical solution of differential equations. This article focuses on calculation of definite integrals. The term numerical quadrature (often abbreviated to quadrature) is more or less a synonym for numerical integration, especially as applied to one-dimensional integrals.
Angular velocityIn physics, angular velocity (symbol ω, sometimes Ω), also known as angular frequency vector, is a pseudovector representation of how the angular position or orientation of an object changes with time, i.e. how quickly an object rotates (spins or revolves) around an axis of rotation and how fast the axis itself changes direction. The magnitude of the pseudovector, , represents the angular speed (or angular frequency), the rate at which the object rotates (spins or revolves).
Four-velocityIn physics, in particular in special relativity and general relativity, a four-velocity is a four-vector in four-dimensional spacetime that represents the relativistic counterpart of velocity, which is a three-dimensional vector in space. Physical events correspond to mathematical points in time and space, the set of all of them together forming a mathematical model of physical four-dimensional spacetime. The history of an object traces a curve in spacetime, called its world line.
