Data for "Block ratio optimized cationic polyacrylamides for enhanced nitrate rejection under applied potential"

README Overview This repository contains the data and input files used in our manuscript's molecular dynamics (MD) simulations: ''Block Ratio Optimized Cationic Polyacrylamides for Enhanced Nitrate Rejection Under Applied Potential.'' https://doi.org/10.1016/j.cej.2025.162346 Citation If you use these files in your own work, please cite our paper: Block Ratio Optimized Cationic Polyacrylamides for Enhanced Nitrate Rejection Under Applied Potential, https://doi.org/10.1016/j.cej.2025.162346 Folder Structure EMD/ – Equilibrium MD Simulations (GROMACS) final_configurations/ Contains the final configuration files (md.gro) for each polymer type: 0:20, 4:16, 8:12, 12:8, 16:4 refer to different block ratios of uncharged to charged monomers. These are representative examples, containing 5 chains of DCPAM at 0.1 M NaNO₃ salt concentration. forcefields/ Contains topology and structure files: - Each block ratio folder includes: - mol.itp: Topology - mol.pdb: Structure - mol.rtp: Residue topology for building - ions_and_water/: Force field files for ions and TIP3P water model: - NO3.itp, NO3.rtp – nitrate ion - NA_and_CL.itp – sodium and chloride ions - tip3p.itp – water model mdp_files/ Standard GROMACS parameter files: - em.mdp: Energy minimization - npt.mdp: NPT equilibration - md.mdp: Production MD run NEMD/ – Non-Equilibrium MD Simulations (LAMMPS) forcefields/ - *.lt: Moltemplate input files for all species (polymers, water, ions, graphene) - graphene.lt: Graphene piston/membrane - TIP3P.lt: Water model - NO3.lt: Nitrate ion - *.lt: Various block copolymer types (same naming convention as the paper) input_files/ - system.in: Main LAMMPS input script - system.in.init: Initialization commands - system.in.settings: Pair and bond coefficients, force field settings Notes - Polymer Types: The numbers in folder names (e.g., 12:8) indicate the ratio of uncharged to charged monomers in each diblock copolymer chain. - Force Field Compatibility: - EMD simulations use GROMACS-compatible .itp and .pdb files. - NEMD simulations are built with Moltemplate and run in LAMMPS. - Water Model: All simulations use the TIP3P water model.