HydroLayer Calculator: A Pseudo-Parallel Tool for Rapid Hydration Layer Structure Calculation in MD Simulations via VMD

Hydration plays a crucial role in the performance of hydrophilic materials, influencing properties such as fouling resistance and lubrication. Characterizing the parameters of the hydration layer is essential to understanding these behaviors. In this study, we developed the HydroLayer Calculator, a multiparameter analysis tool based on Tcl, designed to calculate six key parameters of the hydration layer along the radial direction of the reference atoms using VMD: radial distribution function (RDF), orientation distribution function (ODF), hydrogen bond (HB) structure, mean square displacement (MSD), mean residence time (MRT), and water binding sites (WBS). An innovative pseudoparallel computing method is introduced to significantly enhance computational efficiency while addressing the limitations of existing single-function tools. Application of the tool to molecular dynamics simulations of carboxyethyl methacrylate (CEMA), 2-hydroxyethyl methacrylate (HEMA), glycidyl methacrylate (GMA), and bulk water systems revealed distinct differences in hydration layer dynamics on various surfaces. The tool features a user-friendly modular architecture, supports custom parameter extensions, and can be applied to a wide range of molecular systems and parameter calculations. The HydroLayer Calculator offers significant benefits for researchers studying hydration layers.水合作用对亲水材料的性能发挥至关重要，可影响其抗污性、润滑性等关键属性。表征水合层的各项参数，是理解上述行为机制的核心前提。本研究开发了基于Tcl的多参数分析工具HydroLayer Calculator（水合层计算器），该工具依托VMD软件，可沿参考原子的径向方向计算水合层的六项关键参数：径向分布函数（RDF）、取向分布函数（ODF）、氢键（HB）结构、均方位移（MSD）、平均停留时间（MRT）以及水结合位点（WBS）。本研究引入了一种创新性的伪并行计算方法，在解决现有单功能工具局限性的同时，大幅提升了计算效率。将该工具应用于甲基丙烯酸羧乙酯（CEMA）、甲基丙烯酸羟乙酯（HEMA）、甲基丙烯酸缩水甘油酯（GMA）以及本体水体系的分子动力学模拟后，研究揭示了不同表面上水合层动力学行为的显著差异。该工具具备友好易用的模块化架构，支持自定义参数扩展，可广泛应用于各类分子体系与参数计算场景。HydroLayer Calculator（水合层计算器）为从事水合层研究的科研人员提供了显著助力。