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.