Using computer simulations to study biological problems
The MARTINI force field, developed between the groups of Marrink and Tieleman, is a coarse grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds.
The model uses a four-to-one mapping where, on average, four heavy atoms are represented by a single interaction center. In order to keep the model simple, only four main types of interaction sites are defined: polar (P), non-polar (N), apolar (C), and charged (Q). Each particle type has a number of subtypes, which allow for an accurate representation of the chemical nature of the underlying atomistic structure.
Currently, topologies are available for many lipids and surfactant molecules, including cholesterol, and for all amino acids as well as for sugars and polymers. Scripts are furthermore available to build topologies for arbitrary peptides and proteins, to add elastic networks, and to move between coarse-grained and atomistic representations.
The Martini force field has become one of the most used Coarse Grained force fields in the field of biomolecular molecular dynamics simulations. The original 2004 and 2007 papers have been cited 654 and 608 times, respectively. The force field has been implemented in three major simulations codes (Gromacs, Gromos and NAMD). Notable successes are simulations of the clustering behavior of syntaxin-1A, the simulations of the opening of MscL channels and the simulation of the domain partitioning of membrane peptides.