MERMAID

MERMAID performs coarse-grained molecular dynamics (CGMD) simulations of membrane proteins using the Martini force field to enable study of large conformational changes and dynamic events such as ion channel gating and G-protein-coupled receptor (GPCR) activation.

Key Features:

• Martini force field: Implements the Martini coarse-grained force field for membrane protein simulations.
• Simulation preparation: Generates CGMD-ready setups for membrane protein systems.
• Simulation execution: Executes coarse-grained molecular dynamics (CGMD) simulations of membrane proteins.
• Trajectory analysis: Provides tools to analyze simulation trajectories and extract dynamic information.
• Reduced computational cost: Lowers computational demands relative to atomistic molecular dynamics to enable exploration of long-timescale and large-conformational-change events.

Scientific Applications:

• Membrane protein dynamics: Investigation of conformational changes and dynamic processes in membrane proteins.
• Ion channel gating: Analysis of gating mechanisms in ion channels.
• G-protein-coupled receptor (GPCR) activation: Modeling activation and conformational transitions in GPCRs.
• Pharmacology, structural biology, and biophysics: Supporting studies that link molecular dynamics to functional and structural outcomes in these fields.

Methodology:

Coarse-grained molecular dynamics using the Martini force field, including preparation and execution of CGMD simulations and analysis of resulting trajectories.