Facilitating CG Simulations with MAD: The MArtini Database Server

Area of Science:

• Computational chemistry
• Biophysics
• Materials science

Background:

• The Martini force field is widely used for coarse-grained molecular dynamics (MD) simulations.
• Sharing molecular structures and topologies is crucial for reproducible research.
• Generating input files for complex systems can be time-consuming.

Purpose of the Study:

• To present the MArtini Database (MAD) web server.
• To facilitate the use of the Martini 3 coarse-grained force field.
• To streamline the preparation of molecular systems for MD simulations.

Main Methods:

• The MAD server provides tools for submitting and retrieving coarse-grained (CG) models.
• It converts atomistic structures to CG representations with user-defined control.
• It assembles biomolecules into large systems for simulation.

Main Results:

• MAD supports a wide range of molecules including lipids, carbohydrates, and nanoparticles.
• The server generates input files compatible with the GROMACS MD engine.
• It specifically supports the latest Martini 3 force field.

Conclusions:

• MAD simplifies the creation and sharing of Martini CG models.
• The server accelerates the setup of complex molecular systems for MD simulations.
• MAD enhances the accessibility and application of coarse-grained modeling.