Cyclodextrin-PFAS Simulations

This repository contains molecular dynamics (MD) simulation setups, scripts, and analysis tools to study the interactions between α/β/γ‑cyclodextrins (ACD/BCD/GCD) and various PFAS or interferent molecules (PFOS, SDS, TCAA). The workflow is designed for GROMACS + PLUMED simulations with free‑energy calculations to assess binding and selectivity.

qMD4

This folder contains the .gro and .itp files for setting up cyclodextrins for simulation.

interferents_gaff

This folder contains the .gro and .itp files for setting up interferents for simulation

system_cd

This folder contains all relevant files for simulation of PFAS - Cyclodextrin systems. The folder is subdivided into subfolders containing the required scripts to assemble the simulations, equilibrate the systems and perform the molecular dynamics calculations.

analysis

This folder contains the jupyter notebook and corresponding .py files for computing delta Gs and Kbs for any given system for your choice of grid and cutoff.

📂 Repository Structure

Cyclodextrin-PFAS_Simulations/
│ ├── LICENSE # MIT or chosen license
├── README.md # Project documentation
│ ├── analysis/ # Analysis scripts and notebooks
│ ├── KbdG_samplecalculations.ipynb # Example free-energy/binding calc
│ ├── calculateFES.py # Compute free energy surfaces (FES)
│ └── process-traj-unbiased.sh # Process raw MD trajectories
│ ├── interferents_gaff/ # Force-field (GAFF) for interferent molecules
│ ├── TCAA.* # Trichloroacetic acid (TCAA) inputs
│ ├── sds.* # SDS inputs
│ ├── .sh # Box generation & parameter extraction scripts
│ ├── qMD4/ # Cyclodextrin base parameter files
│ ├── acd.gro/top # α-cyclodextrin
│ ├── bcd/... # β-cyclodextrin with force-field files
│ ├── gcd.gro/top # γ-cyclodextrin
│ ├── ions.itp, water-ffatoms.itp
│ └── system_cd/ # Full MD system setups for each host–guest pair
├── pfos-f- # PFOS with ACD, BCD, GCD
├── sds-f-* # SDS with ACD, BCD, GCD
├── tcaa-f-* # TCAA with ACD, BCD, GCD
│ ├── .gro/top/itp/mdp # Structures & topology
│ ├── plumed.dat # Biasing/collective variable setup
│ ├── taac-.sbatch # Cluster submission scripts
│ ├── reweight*.sh # Free-energy reweighting scripts

• *-f-acd, *-f-bcd, *-f-gcd: PFAS/interferent bound to α, β, γ‑cyclodextrin
  
• *.mdp: Standard GROMACS input files for minimization, equilibration, and production runs
  
• plumed*.dat: PLUMED inputs for biasing
  
• *.sbatch: SLURM job submission scripts for HPC execution
  

Citation

If you use this work please cite:

 @article{Wang_Jang_Topel_2024, 
title={Reversible ppt-Level Detection of Perfluorooctane Sulfonic Acid in Tap Water using Field-Effect Transistor Sensors}, 
author={Wang, Yuqin and Jang, Hyun-June and Topel, Max and Dasetty, Siva and Liu, Yining and Ateia, Mohamed and Tam, Aaron and Rozyyev, Vepa and Ouyang, Ellie and Zhuang, Wen and et al.},
journal={ChemRxiv}, 
year={2024}, 
doi={10.26434/chemrxiv-2024-6q6q5}, 
note={Preprint; not peer-reviewed}, }