Martini 3 Coarse-Grained Force Field: Small Molecules Riccardo Alessandri,∗,y,x Jonathan Barnoud,y,k Anders S. Gertsen,z Ilias Patmanidis,y Alex H. de Vries,y Paulo C. T. Souza,∗,y,{ and Siewert J. Marrink∗,y yGroningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands zDepartment of Energy Conversion and Storage, Technical University of Denmark, Fysikvej 310, DK-2800 Kgs. Lyngby, Denmark {Current address: Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007, Lyon, France xCurrent address: Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States kCurrent address: Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, U.K. E-mail:
[email protected];
[email protected];
[email protected] 1 Abstract The recent re-parametrization of the Martini coarse-grained force field, Martini 3, improved the accuracy of the model in predicting molecular packing and interactions in molecular dynamics simulations. Here, we describe how small molecules can be accurately parametrized within the Martini 3 framework and present a database of validated small molecule models (available at https://github.com/ricalessandri/ Martini3-small-molecules and http://cgmartini.nl). We pay particular atten- tion to the description of aliphatic and aromatic ring-like structures, which are ubiq- uitous in small molecules such as solvents and drugs or in building blocks constituting macromolecules such as proteins and synthetic polymers. In Martini 3, ring-like struc- tures are described by models that use higher resolution coarse-grained particles (small and tiny particles).