title: CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field.
abstract: Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed CHARMM-GUI Martini Maker for building solution, micelle, bilayer, and vesicle systems as well as systems with randomly distributed lipids using the Martini force field. Martini Maker supports 82 lipid types and different flavors of the Martini force field, including polar and nonpolar Martini, Dry Martini, and ElNeDyn (an elastic network model for proteins). The qualities of the systems generated by Martini Maker are validated by simulations of various examples involving proteins and lipids. We expect Martini Maker to be a useful tool for modeling large, complicated biomolecular systems in a user-friendly way.
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States.
authors.forename: Yifei
authors.initials: Y
authors.lastname: Qi
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: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States.
authors.forename: Xi
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States.
authors.forename: Jumin
authors.initials: J
authors.lastname: Lee
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
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States.
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
mesh_terms: D003196:Computer Graphics; D008055:Lipids / Q000737:chemistry*; D008823:Micelles; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D008055:Lipids; D008823:Micelles; D011506:Proteins