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

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Bibliographic Details
Title: HydroLayer Calculator: A Pseudo-Parallel Tool for Rapid Hydration Layer Structure Calculation in MD Simulations via VMD
Authors: Guanghui Cui, Jia Man, Maocheng Ji, Yongqi Zhang, Xinzhong Song, Jianyong Li, Jianfeng Li
Publication Year: 2025
Subject Terms: Biophysics, Biochemistry, Medicine, Cell Biology, Biotechnology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, water binding sites, mean square displacement, friendly modular architecture, molecular dynamics simulations, cema ), hydration layer dynamics, hydration layer along, radial distribution function, hydration layer, radial direction, molecular systems, function tools, mrt ), gma ), wide range, wbs ), various surfaces
Time: 2
Description: 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.
Document Type: article in journal/newspaper
Language: unknown
DOI: 10.1021/acs.jcim.5c01006.s001
Availability: https://doi.org/10.1021/acs.jcim.5c01006.s001
https://figshare.com/articles/journal_contribution/HydroLayer_Calculator_A_Pseudo-Parallel_Tool_for_Rapid_Hydration_Layer_Structure_Calculation_in_MD_Simulations_via_VMD/29672809
Rights: CC BY-NC 4.0
Accession Number: edsbas.EBAB5C5E
Database: BASE
Description
Abstract: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.
DOI:10.1021/acs.jcim.5c01006.s001