Martini 3

Martini 3 provides a coarse-grained molecular dynamics force field for simulating biomolecular and soft‑matter systems.

Key Features:

• Coarse-Grained Representation: Maps groups of atoms into larger beads to enable simulation of large biomolecular systems over extended time scales while preserving essential structural detail.
• Systematic Parametrization: Uses a combination of top-down and bottom-up strategies for parameter development.
• Non-bonded Interactions: Derives non-bonded parameters from experimental partitioning free energies between polar and apolar phases.
• Bonded Interactions: Informs bonded parameters from all-atom simulations.
• Improved Interaction Balance: Introduces new bead types to represent specific interactions such as hydrogen bonding and electronic polarizability for more accurate molecular packing and interactions.
• Expanded Application Range: Supports simulations relevant to oil/water partitioning, miscibility studies, protein-protein and protein-lipid interactions, and materials like ionic liquids and aerogels.

Scientific Applications:

• Partitioning and Miscibility: Modeling of molecular distribution between phases, including oil/water partitioning and miscibility behavior.
• Protein Interactions: Simulation of protein-protein and protein-lipid interactions for studies of biomolecular assembly and membrane processes.
• Material Science: Investigation of soft-matter and materials systems such as ionic liquids and aerogels.

Methodology:

Coarse-graining into beads; parametrization via combined top-down and bottom-up approaches; non-bonded interactions fitted to experimental partitioning free energies between polar and apolar phases; bonded interactions informed by all-atom simulations; incorporation of new bead types to capture hydrogen bonding and electronic polarizability.