How Does Homeoviscous Adaptation of a Lipid Bilayer Influence Interfacial Water Dynamics?

This repository contains the molecular dynamics simulation data, topology and force-field files, simulation parameters, and analysis codes associated with the research article entitled “How Does Homeoviscous Adaptation of a Lipid Bilayer Influence Interfacial Water Dynamics?”, submitted to The Journal of Physical Chemistry B. The repository is organized into four main directories: System_Configurations: Initial and final system configurations (.gro) and molecular dynamics trajectory files (.xtc) for the AHA and BHA systems at 240, 270, and 300 K. Topology_and_Forcefield: Topology (.top) and molecular interaction parameter (.itp) files, including the CHARMM36 force field parameters. Simulation_Parameters: GROMACS molecular dynamics parameter (.mdp) files used for energy minimization, equilibration, annealing, and production simulations. Analysis_Codes: Fortran source codes used for the analysis of interfacial water dynamics, including lateral mean-square displacement, non-Gaussian parameter, rotational correlation functions, survival probability, and hydrogen-bond analysis. Trajectory sampling: The original simulation trajectories were saved at 0.2 ps intervals and were used for the analyses presented in the manuscript. Due to storage constraints, the trajectory files deposited in this repository have been downsampled to 10 ps intervals. The deposited trajectories provide representative simulation configurations and structural information, while the original sampling interval is documented here for clarity. The repository is intended to facilitate transparency, accessibility, and further investigation of the molecular dynamics simulations and analysis methods reported in this study. Software: GROMACS; CHARMM36 force field; Fortran-based analysis codes.