MAD

MAD provides repository and processing capabilities for molecules parameterized with the Martini coarse-grained (CG) force field, enabling conversion of atomistic structures into Martini 3 coarse-grained models and preparation of GROMACS input files for molecular dynamics simulations.

Key Features:

• Sharing and retrieval of structures and topologies: Stores and provides access to structures and topologies parameterized with the Martini coarse-grained (CG) force field, including Martini 3.
• Atomistic-to-coarse-grained conversion: Converts atomistic protein structures into coarse-grained representations using Martini mapping with fine control over the transformation.
• Preparation of complex biological systems: Prepares complex systems such as proteins, lipids, carbohydrates, and nanoparticles for coarse-grained molecular dynamics simulations.
• GROMACS input generation: Generates the necessary input files to initiate simulations with the GROMACS molecular dynamics engine compatible with Martini force fields.
• Support for Martini 3: Implements parameterization and model generation compatible with the Martini 3 force field.

Scientific Applications:

• Large-scale coarse-grained MD simulations: Enables computationally efficient simulation of large biomolecular systems using Martini coarse-graining.
• Membrane dynamics: Facilitates simulation studies of lipid membranes and membrane-associated processes at the CG level.
• Protein folding and conformational sampling: Supports exploration of protein folding pathways and conformational changes using CG models.
• Biomolecular interactions in cellular environments: Allows investigation of interactions among proteins, lipids, carbohydrates, and nanoparticles within CG model systems.
• Standardization of parameterized models: Enables distribution and reuse of parameterized structures and topologies to ensure consistency of simulation parameters across studies.

Methodology:

Converts detailed atomistic structures into simplified coarse-grained representations while preserving essential structural and functional characteristics; provides topologies and structures parameterized with the Martini coarse-grained force field (including Martini 3); enables submission and retrieval of models and fine control over the conversion process; outputs input files for GROMACS simulations.