Introduction to Molecular Dynamics

摘要: Molecular dynamics is the science of simulating time dependent behavior a system particles. The evolution set interacting atoms followed by integrating their equation motion with boundary conditions appropriate for geometry or symmetry system. generate information at microscopic level, which are: atomic positions, velocities. In order to calculate from laws classical mechanics, MD requires, as an input, description interaction potential (or force field). quality results simulation depends on accuracy inter-particle potential. This choice very strongly application. Thus technique acts computational microscope. then converted macroscopic observable like pressure, temperature, heat capacity and stress tensor etc. using statistical mechanics. dynamic techniques have been widely used almost all branches science. Namely, determination reaction rates in chemistry, solid state structures, surfaces defects formation material science, protein folding biochemistry so on. Recent applications employing common fields include exploration pathways solution [1], structural dynamical properties ion channels [2, 3]. disadvantage model force-field that restricted single molecular connectivity. prohibits field models describing chemical processes involving bond breaking forming. An alternative approach combination electronic structure: internuclear forces are computed fly structure calculation proceeds [4, 5]. method, known ab initio dynamics, requires no input capable events, although it has high overhead.