Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
J Comput Chem. 2010 Nov 15;31(14):2593-600. doi: 10.1002/jcc.21552.
Implicit solvent representations, in general, and generalized Born models, in particular, provide an attractive way to reduce the number of interactions and degrees of freedom in a system. The instantaneous relaxation of the dielectric shielding provided by an implicit solvent model can be extremely efficient for high-throughput and Monte Carlo studies, and a reduced system size can also remove a lot of statistical noise. Despite these advantages, it has been difficult for generalized Born implementations to significantly outperform optimized explicit-water simulations due to more complex functional forms and the two extra interaction stages necessary to calculate Born radii and the derivative chain rule terms contributing to the force. Here, we present a method that uses a rescaling transformation to make the standard generalized Born expression a function of a single variable, which enables an efficient tabulated implementation on any modern CPU hardware. The total performance is within a factor 2 of simulations in vacuo. The algorithm has been implemented in Gromacs, including single-instruction multiple-data acceleration, for three different Born radius models and corresponding chain rule terms. We have also adapted the model to work with the virtual interaction sites commonly used for hydrogens to enable long-time steps, which makes it possible to achieve a simulation performance of 0.86 micros/day for BBA5 with 1-nm cutoff on a single quad-core desktop processor. Finally, we have also implemented a set of streaming kernels without neighborlists to accelerate the non-cutoff setup occasionally used for implicit solvent simulations of small systems.
隐溶剂表示法，一般而言，和广义 Born 模型，特别是，提供了一种减少系统中相互作用和自由度数量的有吸引力的方法。隐溶剂模型提供的介电屏蔽的瞬时弛豫对于高通量和蒙特卡罗研究非常有效，并且较小的系统尺寸也可以消除大量的统计噪声。尽管有这些优势，但由于更复杂的函数形式以及计算 Born 半径和对力有贡献的导数链式规则项所需的额外两个相互作用阶段，广义 Born 实现很难显著优于优化的显式水模拟。在这里，我们提出了一种使用缩放变换的方法，将标准广义 Born 表达式转换为单个变量的函数，从而可以在任何现代 CPU 硬件上实现高效的表格实现。总性能与真空中的模拟相差 2 倍以内。该算法已在 Gromacs 中实现，包括单指令多数据加速，用于三种不同的 Born 半径模型和相应的链式规则项。我们还对模型进行了修改，使其能够与通常用于氢的虚拟相互作用位点一起使用，从而能够实现具有 1nm 截止的 BBA5 的 0.86 微秒/天的模拟性能单个四核桌面处理器。最后，我们还实现了一组没有邻居列表的流核，以加速偶尔用于小系统隐溶剂模拟的非截止设置。
