title: Molecular dynamics simulations of lipid bilayers: simple recipe of how to do it.
abstract: 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.
authors.affiliation: Department of Physics, Tampere University of Technology, Tampere, Finland.
authors.forename: Hector
authors.initials: H
authors.lastname: Martinez-Seara
authors.forename: Tomasz
authors.initials: T
authors.lastname: Róg
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry / Q000378:metabolism; D002462:Cell Membrane / Q000737:chemistry / Q000378:metabolism; D003903:Deuterium / Q000737:chemistry; D004058:Diffusion; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D015203:Reproducibility of Results; D012399:Rotation; D012984:Software
chemical_list: D008051:Lipid Bilayers; D015060:1,2-Dipalmitoylphosphatidylcholine; D003903:Deuterium