Grotz Kara K, Schwierz Nadine
Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main, Germany.
J Chem Phys. 2022 Mar 21;156(11):114501. doi: 10.1063/5.0087292.
Magnesium plays a vital role in a large variety of biological processes. To model such processes by molecular dynamics simulations, researchers rely on accurate force field parameters for Mg and water. OPC is one of the most promising water models yielding an improved description of biomolecules in water. The aim of this work is to provide force field parameters for Mg that lead to accurate simulation results in combination with OPC water. Using 12 different Mg parameter sets that were previously optimized with different water models, we systematically assess the transferability to OPC based on a large variety of experimental properties. The results show that the Mg parameters for SPC/E are transferable to OPC and closely reproduce the experimental solvation free energy, radius of the first hydration shell, coordination number, activity derivative, and binding affinity toward the phosphate oxygens on RNA. Two optimal parameter sets are presented: MicroMg yields water exchange in OPC on the microsecond timescale in agreement with experiments. NanoMg yields accelerated exchange on the nanosecond timescale and facilitates the direct observation of ion binding events for enhanced sampling purposes.
镁在各种各样的生物过程中起着至关重要的作用。为了通过分子动力学模拟对这些过程进行建模,研究人员依赖于针对镁和水的精确力场参数。OPC是最有前景的水模型之一,能对水中的生物分子给出更好的描述。这项工作的目的是提供与OPC水结合时能产生精确模拟结果的镁的力场参数。我们使用先前用不同水模型优化过的12种不同的镁参数集,基于大量实验性质系统地评估其向OPC的可转移性。结果表明,SPC/E的镁参数可转移到OPC,并能紧密重现实验溶剂化自由能、第一水合壳层半径、配位数、活度导数以及对RNA上磷酸氧的结合亲和力。本文给出了两个最优参数集:MicroMg在微秒时间尺度上能在OPC中实现与实验一致的水交换。NanoMg在纳秒时间尺度上能实现加速交换,并便于直接观察离子结合事件以用于增强采样目的。