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Monte Carlo molecular modeling
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<p>Monte Carlo molecular modelling is the application of <a href="/facts/Monte_Carlo_method/AkHjY7jc">Monte Carlo methods</a> to molecular problems. These problems can also be modelled by the <a href="/facts/Molecular_dynamics/yR3DNt6U">molecular dynamics</a> method. The difference is that this approach relies on <a href="/facts/Equilibrium_statistical_mechanics/6zMsNYYG">equilibrium statistical mechanics</a> rather than molecular dynamics. Instead of trying to reproduce the dynamics of a system, it generates states according to appropriate <a href="/facts/Boltzmann_distribution/XBU530uu">Boltzmann distribution</a>. Thus, it is the application of the Metropolis Monte Carlo simulation to molecular systems. It is therefore also a particular subset of the more general <a href="/facts/Monte_Carlo_method_in_statistical_physics/INfKT5uB">Monte Carlo method in statistical physics</a>. </p><p>It employs a <a href="/facts/Markov_chain/5oP5hntk">Markov chain</a> procedure in order to determine a new state for a system from a previous one. According to its stochastic nature, this new state is accepted at random. Each trial usually counts as a move. The avoidance of dynamics restricts the method to studies of static quantities only, but the freedom to choose moves makes the method very flexible. These moves must only satisfy a basic condition of balance in order for the equilibrium to be properly described, but <a href="/facts/Detailed_balance/qVpGh7HW">detailed balance</a>, a stronger condition, is usually imposed when designing new algorithms. An additional advantage is that some systems, such as the <a href="/facts/Ising_model/lvBpj2h1">Ising model</a>, lack a dynamical description and are only defined by an energy prescription; for these the Monte Carlo approach is the only one feasible. </p><p>The great success of this method in statistical mechanics has led to various generalizations such as the method of <a href="/facts/Simulated_annealing/JCmHqd3t">simulated annealing</a> for optimization, in which a fictitious temperature is introduced and then gradually lowered. </p><p>A range of software packages have been developed specifically for the use of the Metropolis Monte Carlo method on molecular simulations. These include: </p> <ul><li>BOSS</li> <li><a href="/facts/CP2K/g84Xktgq">CP2K</a></li> <li>MCPro</li> <li>Sire</li> <li>ProtoMS</li> <li>Faunus</li></ul>