Humana Press, Methods in Molecular Biology, p. 407-429, 2012
DOI: 10.1007/978-1-62703-017-5_15
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Simulations based on molecular dynamics (MD) are an important tool in structural biology. In the field of lipid membrane research, MD represents a major tool as it grant access to atomic level features of the membrane difficult to access by experimental means. In this chapter we describe step by step how to simulate a membrane in silico. The explanation comprehends from the initial set up of a membrane system to its analysis passing through the simulation itself. Most of the tasks described here are performed using the Gromacs simulation suite, a widely used software for molecular modeling and simulations. In the selected example the attention is focused on a single component lipid bilayer composed of DPPC, one of the most studied lipid species.