GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems

• Published in: Nature communications Vol. 15; no. 1; p. 3370
• Main Authors: Jung, Jaewoon, Tan, Cheng, Sugita, Yuji
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 20.04.2024; Nature Publishing Group UK; Nature Portfolio
• Subjects: Biological activity; Biomolecules; Computational efficiency; Computer applications; Computing time; Decomposition; Domain decomposition methods; Droplets; Dynamic loads; Load balancing; Microscopy; Molecular dynamics; Molecular Dynamics Simulation; Nucleic Acids; Ostwald ripening; Particle distribution; Proteins; Residues; Simulation; Software
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-47654-1

Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models.