用树码求和和截断加速分子溶剂化的3D- RISM理论
Accelerating the 3D-RISM theory of molecular solvation with treecode summation and cut-offs
摘要：
分子溶剂化的三维参考相互作用位点模型（3D-RISM）是计算溶质分子周围溶剂（如水和共离子）的平衡热力学和密度分布的有力工具。然而，3D-RISM解决方案的计算成本可能很高，特别是对于蛋白质和其他大分子，其中计算溶质和溶剂之间的势能需要一半以上的计算时间。为了解决这个问题，我们已经开发并实现了长程相互作用的树码求和和短程相互作用的分析校正截止值，以加速AmberTools分子建模套件中非周期性3D-RISM中的势能和长程渐近计算。对于这项工作中考虑的最大的单一蛋白质微管蛋白，总计算时间减少了4倍。此外，这些新方法的并行计算几乎是线性扩展的，迭代求解器仍然是并行扩展的最大障碍。为了证明我们的方法在大系统中的实用性，我们使用3D-RISM计算了由910个微管蛋白二聚体，超过120万个原子组成的7环微管的溶剂化热力学和密度分布。
英文摘要：
The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However, 3D-RISM solutions can be expensive to calculate, especially for proteins and other large molecules where calculating the potential energy between solute and solvent requires more than half the computation time. To address this problem, we have developed and implemented treecode summation for long-range interactions and analytically corrected cut-offs for short-range interactions to accelerate the potential energy and long-range asymptotics calculations in non-periodic 3D-RISM in the AmberTools molecular modeling suite. For the largest single protein considered in this work, tubulin, the total computation time was reduced by a factor of 4. In addition, parallel calculations with these new methods scale almost linearly and the iterative solver remains the largest impediment to parallel scaling. To demonstrate the utility of our approach for large systems, we used 3D-RISM to calculate the solvation thermodynamics and density distribution of 7-ring microtubule, consisting of 910 tubulin dimers, over 1.2 million atoms.
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