An accurate depiction of electrostatic interactions in molecular dynamics requires the correct number of ions in the simulation box to capture screening effects. However, the number of ions that should be added to the box is seldom given by the bulk salt concentration because a charged biomolecule solute will perturb the local solvent environment. We present a simple method for calculating the number of ions that requires only the total solute charge, solvent volume, and bulk salt concentration as inputs. We show that the most commonly used method for adding salt to a simulation results in an effective salt concentration that is too high. These findings are confirmed using simulations of lysozyme. We have established a web server where these calculations can be readily performed to aid simulation setup.

中文翻译：

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SLTCAP：一种简单的方法，用于计算MD仿真所需的离子数

分子动力学中静电相互作用的准确描述需要模拟框中的离子数量正确才能捕获筛选效果。但是，由于大分子盐浓度很少给出应添加到盒子中的离子数量，因为带电荷的生物分子溶质会干扰当地的溶剂环境。我们提出一种简单的方法来计算离子数，仅需要总溶质电荷，溶剂体积和总盐浓度作为输入。我们表明，最常用的向模拟中添加盐的方法会导致有效盐浓度过高。使用溶菌酶的模拟证实了这些发现。我们已经建立了一个Web服务器，可以在其中轻松进行这些计算，以帮助进行仿真设置。