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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

Abstract

We 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.


The full paper is available here.

The book is available from MIT Press and also at amazon.