Martini is a coarse-grained (CG) force field developed by Marrink and coworkers at the University of Groningen, initially developed in 2004 for molecular dynamics simulation of lipids, later (2007) extended to various other molecules. The force field applies a mapping of four heavy atoms to one CG interaction site and is parametrized with the aim of reproducing thermodynamic properties.
Contents
Philosophy
For the Martini force field 4 bead categories have been defined: Q (charged), P (polar), N (nonpolar), and C (apolar). These bead types are in turn split in 4 or 5 different levels, giving a total of 20 beadtypes. For the interactions between the beads, 10 different interaction levels are defined (O-IX). The beads can be used at normal size (4:1 mapping) or S-size (small, 3:1 mapping). The latter is mainly used in ring structures. Bonded interactions (bonds, angles, dihedrals, and impropers) are derived from atomistic simulations of crystal structures.
Use
The Martini force field has become one of the most used coarse grained force fields in the field of molecular dynamics simulations for biomolecules. The original 2004 and 2007 papers have been cited 654 and 608 times, respectively. The force field has been implemented in three major simulation codes: GROningen MAchine for Chemical Simulations (GROMACS), GROningen MOlecular Simulation (GROMOS), and Nanoscale Molecular Dynamics (NAMD). Notable successes are simulations of the clustering behavior of syntaxin-1A, the simulations of the opening of mechanosensitive channels (MscL) and the simulation of the domain partitioning of membrane peptides.
Lipids
The initial papers contained parameters for water, simple alkanes, organic solvents, surfactants, a wide range of lipids and cholesterol. They semiquantitatively reproduce the phase behavior of bilayers with other bilayer properties, and more complex bilayer behavior.
Proteins
Compatible parameters for proteins were introduced by Monticelli et al.. Secondary structure elements, like alpha helixes and beta sheets (β-sheets), are constrained. Martini proteins are often simulated in combination with an elastic network, such as Elnedyn, to maintain the overall structure.
Carbohydrates
Compatible parameters were released in 2009.
Other
Parameters for different other molecules are available from the Martini website.