Cantero Jorge, Ballesteros-Casallas Andrés, Santos Lucianna H S, Paulino Margot, Pantano Sergio
Área Bioinformática, Departamento DETEMA, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11600, Uruguay.
Centro de Investigaciones Médicas, Facultad de Ciencias de la Salud, Universidad Nacional del Este, Panambi 101305, Paraguay.
J Phys Chem B. 2024 Dec 5;128(48):11971-11980. doi: 10.1021/acs.jpcb.4c03278. Epub 2024 Sep 25.
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.
分子动力学（MD）模拟为在原子分辨率下探索复杂生物分子系统的动力学提供了一个非常有价值的平台。然而，力场与MD软件引擎之间的兼容性问题可能会限制模拟的互操作性和可转移性。这项工作展示了粗粒度的SIRAH力场在广泛使用的NAMD MD引擎上，成功应用于一系列日益复杂的生物分子系统。通过利用NAMD读取AMBER输入文件的能力，SIRAH模拟可以在NAMD上无缝运行，包括其最近发布的GPU加速版本NAMD3。基准系统在AMBER、NAMD2和NAMD3上展示了一致的结果。因此，这些数据突出了使用这三个引擎以及SIRAH在GPU加速的台式计算机上可实现的更高模拟通量。总体而言，本研究通过利用先进的GPU计算资源和高性能超级计算设施扩展了SIRAH力场的应用范围，这些资源与NAMD配合使用时特别有效。
