explicit solvent

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• Implicit solvation — (sometimes known as continuum solvation) is a method of representing solvent as a continuous medium instead of individual “explicit” solvent molecules most often used in molecular dynamics simulations and in other applications of molecular… …   Wikipedia

• Molecular dynamics — (MD) is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms. In the most common version, the trajectories of molecules… …   Wikipedia

• Molecular modelling — The backbone dihedral angles are included in the molecular model of a protein. Modelling of ionic li …   Wikipedia

• Periodic boundary conditions — In molecular dynamics, periodic boundary conditions (PBC) are a set of boundary conditions used to simulate an effectively infinitely tiled system, usually applied to systems consisting of one or more macromolecules in a bath of explicit solvent …   Wikipedia

• Flying ice cube — In molecular dynamics (MD) simulations, the flying ice cube effect is a numerical integration artifact in which the energy of high frequency fundamental modes is drained into low frequency modes, particularly into zero frequency motions such as… …   Wikipedia

• Chemical file format — This article discusses some common molecular file formats, including usage and converting between them. Contents 1 Distinguishing formats 2 Chemical Markup Language 3 Protein Data Bank Format 4 G …   Wikipedia

• Schizophyllan — is a neutral extracellular polysaccharide produced by the fungus Schizophyllan commune , consisting of a 1,3 β D linked backbone of glucose residues with 1,6 β D glucosyl side groups. The non degraded polysaccharide has a molecular weight of the… …   Wikipedia

• analysis — /euh nal euh sis/, n., pl. analyses / seez /. 1. the separating of any material or abstract entity into its constituent elements (opposed to synthesis). 2. this process as a method of studying the nature of something or of determining its… …   Universalium

• Flory-Huggins solution theory — is a mathematical model of the thermodynamics of polymer solutions which takes account of the great dissimilarity in molecular sizes in adapting the usual expression for the entropy of mixing. The result is an equation for the Gibbs free energy… …   Wikipedia

• Multi-particle collision dynamics — (MPC), also known as stochastic rotation dynamics (SRD)[1], is a particle based mesoscale simulation technique for complex fluids which fully incorporates thermal fluctuations and hydrodynamic interactions.[2] Coupling of embedded particles to… …   Wikipedia

• bank — bank1 /bangk/, n. 1. a long pile or heap; mass: a bank of earth; a bank of clouds. 2. a slope or acclivity. 3. Physical Geog. the slope immediately bordering a stream course along which the water normally runs. 4. a broad elevation of the sea… …   Universalium