iGEM Plastics Modelling 🧬♻️

This repository contains molecular modelling and simulation files for common plastic polymers developed as part of the iGEM 2024 – REC Chennai project.

The models are designed to support computational analysis of plastic–biological interactions, aiding our efforts to understand and engineer plastic degradation mechanisms.

🌐 Project Wiki:
https://2024.igem.wiki/rec-chennai/model

---

📦 Polymers Included

The repository currently contains simulation setups for:

• Polyethylene (PE)
• Polypropylene (PP)
• Polystyrene (PS)

Each polymer includes structures and simulation input files for different molecular dynamics stages.

---

📁 File Description

Structure Files (.gro)

• minPE.gro, minPP.gro, minPS.gro
  → Energy-minimized structures

• meltPP.gro, meltPS.gro
  → Melted polymer configurations

• productionPE.gro, productionPP.gro, productionPS.gro
  → Final production-ready structures

---

Simulation Parameters (.mdp)

• min*.mdp
  → Energy minimization parameters

• pre_NpT-*.mdp
  → Pre-equilibration under NPT ensemble

---

Topology Files (.top)

• topologyPE.top
• topologyPP.top
• topologyPS.top

These define bonded and non-bonded interactions required for running simulations in GROMACS.

---

🧪 Simulation Software

• Molecular Dynamics Engine: GROMACS
• Force Field: Coarse-grained polymer models (Martini-compatible)

⚠️ Ensure correct force-field files are present in your GROMACS installation before running simulations.

---

🚀 How to Use

1. Clone the repository:

    git clone https://github.com/lokaaaaaaa/iGEM-plastics-modelling.git
   cd iGEM-plastics-modelling
   

Run energy minimization:

gmx grompp -f minPE.mdp -c minPE.gro -p topologyPE.top -o em.tpr gmx mdrun -deffnm em git clone https://github.com/lokaaaaaaa/iGEM-plastics-modelling.git cd iGEM-plastics-modelling