Department of Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom.
J Phys Chem Lett. 2022 May 12;13(18):4046-4051. doi: 10.1021/acs.jpclett.2c00544. Epub 2022 Apr 29.
pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.
生化系统中存在大量的 pH 依赖性；然而，许多用于研究这些系统的模拟方法并没有考虑到这一特性。我们使用改进后的混合非平衡分子动力学（MD）/蒙特卡罗算法，包括一种随机电荷中和方法，该方法特别适用于 MARTINI 力场，并能够在静电计算中实现无伪影的 Ewald 求和方法。我们通过重现先前在实验文献中报道的 pH 依赖性自组装和自组织行为来证明该方法的有效性。此外，我们还进行了油酸滴定实验，我们以一种比以前更相关的方式报告结果，以便与计算方法进行比较。
