Pouring SIRAH on NAMD

• Published in: The journal of physical chemistry. B 2024-12, Vol.128 (48), p.11971-11980
• Main Authors: Cantero, Jorge, Ballesteros-Casallas, Andrés, Santos, Lucianna H. S., Paulino, Margot, Pantano, Sergio
• Format: Article
• Language: English
• Subjects: B: Soft Matter, Fluid Interfaces, Colloids, Polymers, and Glassy Materials; Molecular Dynamics Simulation; Software
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/acs.jpcb.4c03278

Molecular dynamics (MD) simulations provide an invaluable platform for exploring the dynamics of complex biomolecular systems at atomic resolution. However, compatibility issues between force fields and MD software engines can limit the interoperability and transferability of simulations. This work demonstrates the successful use of the coarse-grained SIRAH force field on the widely used NAMD MD engine across a range of increasingly complex biomolecular systems. By leveraging NAMD’s ability to read AMBER input files, SIRAH simulations can be run seamlessly on NAMD, including its recently released GPU-accelerated version, NAMD3. The benchmark systems demonstrate consistent results across AMBER, NAMD2, and NAMD3. Thus, these data highlight the enhanced simulation throughput achievable on GPU-accelerated desktop computers using all three engines along with SIRAH. Overall, this study expands the range of the SIRAH force field by utilizing advanced GPU computing resources and high-performance supercomputing facilities, which are particularly effective with NAMD.