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.
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.
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.
Euler methodIn mathematics and computational science, the Euler method (also called the forward Euler method) is a first-order numerical procedure for solving ordinary differential equations (ODEs) with a given initial value. It is the most basic explicit method for numerical integration of ordinary differential equations and is the simplest Runge–Kutta method. The Euler method is named after Leonhard Euler, who first proposed it in his book Institutionum calculi integralis (published 1768–1870).
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.
Iterative methodIn computational mathematics, an iterative method is a mathematical procedure that uses an initial value to generate a sequence of improving approximate solutions for a class of problems, in which the n-th approximation is derived from the previous ones. A specific implementation with termination criteria for a given iterative method like gradient descent, hill climbing, Newton's method, or quasi-Newton methods like BFGS, is an algorithm of the iterative method.
Linear mapIn mathematics, and more specifically in linear algebra, a linear map (also called a linear mapping, linear transformation, vector space homomorphism, or in some contexts linear function) is a mapping between two vector spaces that preserves the operations of vector addition and scalar multiplication. The same names and the same definition are also used for the more general case of modules over a ring; see Module homomorphism. If a linear map is a bijection then it is called a .
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
Newton's methodIn numerical analysis, Newton's method, also known as the Newton–Raphson method, named after Isaac Newton and Joseph Raphson, is a root-finding algorithm which produces successively better approximations to the roots (or zeroes) of a real-valued function. The most basic version starts with a single-variable function f defined for a real variable x, the function's derivative f′, and an initial guess x0 for a root of f. If the function satisfies sufficient assumptions and the initial guess is close, then is a better approximation of the root than x0.
System of linear equationsIn mathematics, a system of linear equations (or linear system) is a collection of one or more linear equations involving the same variables. For example, is a system of three equations in the three variables x, y, z. A solution to a linear system is an assignment of values to the variables such that all the equations are simultaneously satisfied. A solution to the system above is given by the ordered triple since it makes all three equations valid. The word "system" indicates that the equations should be considered collectively, rather than individually.
Computational chemistryComputational 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.
Uniform convergenceIn the mathematical field of analysis, uniform convergence is a mode of convergence of functions stronger than pointwise convergence. A sequence of functions converges uniformly to a limiting function on a set as the function domain if, given any arbitrarily small positive number , a number can be found such that each of the functions differs from by no more than at every point in .
Holonomic constraintsIn classical mechanics, holonomic constraints are relations between the position variables (and possibly time) that can be expressed in the following form: where are n generalized coordinates that describe the system (in unconstrained configuration space). For example, the motion of a particle constrained to lie on the surface of a sphere is subject to a holonomic constraint, but if the particle is able to fall off the sphere under the influence of gravity, the constraint becomes non-holonomic.
Linear independenceIn the theory of vector spaces, a set of vectors is said to be if there exists no nontrivial linear combination of the vectors that equals the zero vector. If such a linear combination exists, then the vectors are said to be . These concepts are central to the definition of dimension. A vector space can be of finite dimension or infinite dimension depending on the maximum number of linearly independent vectors. The definition of linear dependence and the ability to determine whether a subset of vectors in a vector space is linearly dependent are central to determining the dimension of a vector space.
Constraint programmingConstraint programming (CP) is a paradigm for solving combinatorial problems that draws on a wide range of techniques from artificial intelligence, computer science, and operations research. In constraint programming, users declaratively state the constraints on the feasible solutions for a set of decision variables. Constraints differ from the common primitives of imperative programming languages in that they do not specify a step or sequence of steps to execute, but rather the properties of a solution to be found.
Pointwise convergenceIn mathematics, pointwise convergence is one of various senses in which a sequence of functions can converge to a particular function. It is weaker than uniform convergence, to which it is often compared. Suppose that is a set and is a topological space, such as the real or complex numbers or a metric space, for example. A net or sequence of functions all having the same domain and codomain is said to converge pointwise to a given function often written as if (and only if) The function is said to be the pointwise limit function of the Sometimes, authors use the term bounded pointwise convergence when there is a constant such that .
Radius of convergenceIn mathematics, the radius of convergence of a power series is the radius of the largest disk at the center of the series in which the series converges. It is either a non-negative real number or . When it is positive, the power series converges absolutely and uniformly on compact sets inside the open disk of radius equal to the radius of convergence, and it is the Taylor series of the analytic function to which it converges.
Constraint logic programmingConstraint logic programming is a form of constraint programming, in which logic programming is extended to include concepts from constraint satisfaction. A constraint logic program is a logic program that contains constraints in the body of clauses. An example of a clause including a constraint is . In this clause, is a constraint; A(X,Y), B(X), and C(Y) are literals as in regular logic programming. This clause states one condition under which the statement A(X,Y) holds: X+Y is greater than zero and both B(X) and C(Y) are true.
Compact convergenceIn mathematics compact convergence (or uniform convergence on compact sets) is a type of convergence that generalizes the idea of uniform convergence. It is associated with the compact-open topology. Let be a topological space and be a metric space. A sequence of functions is said to converge compactly as to some function if, for every compact set , uniformly on as . This means that for all compact , If and with their usual topologies, with , then converges compactly to the constant function with value 0, but not uniformly.
Lagrangian mechanicsIn physics, Lagrangian mechanics is a formulation of classical mechanics founded on the stationary-action principle (also known as the principle of least action). It was introduced by the Italian-French mathematician and astronomer Joseph-Louis Lagrange in his 1788 work, Mécanique analytique. Lagrangian mechanics describes a mechanical system as a pair consisting of a configuration space and a smooth function within that space called a Lagrangian. For many systems, where and are the kinetic and potential energy of the system, respectively.
