Transpoly

A reproducible molecular simulation pipeline for polymer/salt systems.

Transpoly automates the workflow from a single-chain protein structure to a packed, solvated GROMACS system, through multistage equilibration, production MD, and comprehensive analysis including ion transport metrics and coordination statistics.

What you will need

• A .pdb file for a single chain
• Can use CHARMM-GUI's polymer builder (https://pubs.acs.org/doi/10.1021/acs.jctc.1c00169) for obtaining a single polymer chain
• If you want to simulate a crosslinked matrix, obtain a non-crosslinked chain from CHARMM-GUI and manually add crosslinking atoms on the single chain using tools like Avogadro (https://avogadro.cc/)

User inputs

• Box dimensions
• Ions to consider
• Target density/ Number of chains to fill

Quick Start

See docs/SETUP.md for environment setup and docs/USAGE.md for pipeline execution.

Requirements

• AmberTools (antechamber, parmchk2, tleap): can also use ab initio MD / DFT (Density Functional Theory calculations) output files
• GROMACS
• Packmol
• Acpype
• Python 3.8+

Pipeline Overview

1. Parameterization: Convert single-chain PDB to Amber topology using GAFF2
2. Packing: Fill simulation box with multiple chains using Packmol
3. GROMACS Prep: Convert to GROMACS with OPLS-AA/AMBER99sb-ildn force field
4. Solvation & Ions: Add water (TIP4P), KCl, NH4Cl, and neutralize
5. Equilibration: Multistage equilibration (EM → NVT → NPT)
6. Production: 10 ns NVT ensemble dynamics
7. Analysis: Ion transport, coordination numbers, RDF, diffusivity estimates

Repository Structure

transpoly/
├── src/transpoly/          # Core Python modules
├── workflows/              # Stage-specific runners
├── templates/              # .mdp, tleap, packmol templates
├── analysis/               # Post-processing and plotting
├── examples/               # Minimal runnable examples
├── docs/                   # Documentation
├── requirements.txt        # Python dependencies
└── README.md

License

See LICENSE file.