Introduction to Molecular simulation
Petr Sulc, Jonathan P.K. Doye, and Ard A. Louis
in "Quantitative Biology: Theory, Computational Methods and Models", ed. B. Munsky, W.S. Hlavacek and L.S. Tsimring (MIT Press, 2018), pp. 179-208
AbstractWe introduce the basic concepts and methods of molecular simulation: the Monte Carlo method and molecular dynamics with Verlet integration scheme along with the commonly used thermostats to control the temperature during simulation. We discuss estimation of errors in measured quantities and introduce common techniques used in molecular simulations: reduced units, periodic boundary conditions, parallelization, and Verlet list and cell lists that allow one to keep efficiently track of interacting particles. We further describe some advanced methods for efficient simulations and speeding-up equilibration (umbrella sampling, parallel tempering and forward flux sampling). Finally, we provide a list of popular simulation software packages.
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