title: Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations.
abstract: For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complementary method for reverse transformation, at http://cgmartini.nl/ . This work highlights the key features of insane and presents a survey of properties for a large range of lipids as a start of a computational lipidomics project.
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.|Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91052 Erlangen, Germany.
authors.forename: Tsjerk A
authors.initials: TA
authors.lastname: Wassenaar
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Helgi I
authors.initials: HI
authors.lastname: Ingólfsson
authors.affiliation: Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91052 Erlangen, Germany.
authors.forename: Rainer A
authors.initials: RA
authors.lastname: Böckmann
authors.affiliation: Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
authors.forename: D Peter
authors.initials: DP
authors.lastname: Tieleman
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Siewert J
authors.initials: SJ
authors.lastname: Marrink
mesh_terms: D005732:Gangliosides / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D010713:Phosphatidylcholines / Q000737:chemistry
chemical_list: D005732:Gangliosides; D008051:Lipid Bilayers; D008565:Membrane Proteins; D010713:Phosphatidylcholines; C028694:1-palmitoyl-2-oleoylphosphatidylcholine