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They are designed to match a set of specific target distributions from the atomistic simulations, using iterative Boltzmann, developed by the groups of Marrink and Tieleman, has also been derived in close connection with atomistic models, especially for bonded interactions.However, the philosophy of our coarse-graining approach is different.The name ‘Martini’ for the force field was coined in 2007 with the release of version 2.0 for lipids.have developed CG protein force fields compatible with the Martini lipid force field, but different from the Martini protein force field.The four-to-one mapping was chosen as an optimum between computational efficiency on the one hand and chemical representability on the other hand. In all cases Martini CG beads are shown as cyan transparent beads overlaying the atomistic structure.Mapping of water is consistent with this choice, as four real water molecules are mapped to a CG water bead. Based on the chemical nature of the underlying structure, the CG beads are assigned a specific particle type with more or less polar character.The non-bonded interactions are cut off at a distance .

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The overall aim of our coarse-graining approach is to provide a simple model that is computationally fast and easy to use, yet flexible enough to be applicable to a large range of biomolecular systems.

Ions are represented by a single CG bead, which represents both the ion and its first hydration shell. The Martini model has four main types of particle: polar (P), non-polar (N), apolar (C), and charged (Q).

To represent the geometry of small ring-like fragments or molecules (, benzene, cholesterol, and several of the amino acids), the general four-to-one mapping approach is too coarse. Within each type, subtypes are distinguished either by a letter denoting the hydrogen-bonding capabilities (d = donor, a = acceptor, da = both, 0 = none) or by a number indicating the degree of polarity (from 1 = low polarity to 5 = high polarity), giving a total of 18 particle types or ‘building blocks’.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.

E-mail: [email protected]; Fax: 398; Tel: 457Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. E-mail: [email protected]; Fax: 1-403-2899311; Tel: 1-403-2202966The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago.

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