Parallel Generalized Born Implicit Solvent Calculations with NAMD

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• 作者：David E. Tanner ; Kwok-Yan Chan ; James C. Phillips ; Klaus Schulten
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2011
• 出版时间：November 8, 2011
• 年：2011
• 卷：7
• 期：11
• 页码：3635-3642
• 全文大小：941K
• 年卷期：v.7,no.11(November 8, 2011)
• ISSN：1549-9626

文摘

Accurate electrostatic descriptions of aqueous solvent are critical for simulation studies of biomolecules, but the computational cost of explicit treatment of solvent is very high. A computationally more feasible alternative is a generalized Born implicit solvent description which models polar solvent as a dielectric continuum. Unfortunately, the attainable simulation speedup does not transfer to the massive parallel computers often employed for simulation of large structures. Longer cutoff distances, spatially heterogeneous distribution of atoms, and the necessary 3-fold iteration over atom pairs in each timestep combine to challenge efficient parallel performance of generalized Born implicit solvent algorithms. Here, we report how NAMD, a parallel molecular dynamics program, meets the challenge through a unique parallelization strategy. NAMD now permits efficient simulation of large systems whose slow conformational motions benefit most from implicit solvent descriptions due to the inherent low viscosity. NAMD鈥檚 implicit solvent performance is benchmarked and then illustrated in simulating the ratcheting Escherichia coli ribosome involving 250鈥?00 atoms.