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.

2025