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.
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References
Mouritsen OG (2004) Life—as a matter of fat: the emerging science of lipidomics. Springer, Berlin
Róg T, Pasenkiewicz-Gierula M, Vattulainen I, Karttunen M (2009) Ordering effects of cholesterol and its analogues. Biochim Biophys Acta 1788:97–121
Marrink SJ, de Vries AH, Tieleman DP (2009) Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim Biophys Acta 1788:149–168
Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447
Humphrey W, Dalke A, Schulten K (1996) VMD—visual molecular dynamics. J Mol Graph 14:33–38
Kukol A (2009) Lipid models for united-atom molecular dynamics simulations of proteins. J Chem Theory Comput 5:615–626
Falck E, Patra M, Karttunen M, Hyvönen MT, Vattulainen I (2004) Lessons of slicing membranes: interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers. Biophys J 87:1076–1091
Zhao W, Róg T, Gurtovenko AA, Vattulainen I, Karttunen M (2007) Structure and electrostatics of POPG lipid bilayers with Na+ counterions: molecular dynamics simulation. Biophys J 92:1114–1124
Falck E, Róg T, Karttunen M, Vattulainen I (2008) Lateral diffusion in lipid membranes through collective flows. J Am Chem Soc 130:44–45
Hess B (2002) Determining the shear viscosity of model liquids from molecular dynamics simulations. J Chem Phys 116:209–217
Nagle JF, Tristram-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta 1469:159–195
Acknowledgments
We wish to acknowledge the Academy of Finland for financial support and CSC—IT Centre for Science (Finland) for computational resources. We also want to thank the Danish Centre for Scientific Computing for providing us access to the Horseshoe supercluster at the University of Southern Denmark (DCSC/SDU).
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Martinez-Seara, H., Róg, T. (2013). Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It. In: Monticelli, L., Salonen, E. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 924. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-017-5_15
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DOI: https://doi.org/10.1007/978-1-62703-017-5_15
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