Polymer Electrolyte Modeling and Discovery (PEMD)

Polymer Electrolyte Modeling and Discovery (PEMD) is a Python toolkit for building, simulating, and analyzing solid polymer electrolytes. It supports an end-to-end workflow spanning four core stages: polymer structure generation, OPLS-AA force-field parameterization, multiscale simulation, and physicochemical property analysis.

Table of Contents

• Key Features
• Repository Structure
• Getting Started
  • Prerequisites
  • Installation
  • Quick Start
• Workflows
• Analysis Toolkit
• Development
• Citation
• License
• Contact

Key Features

• Polymer builders – Generate homo- and co-polymer structures directly from JSON configuration files using PEMD.core.model.PEMDModel. Automated Packmol integration produces amorphous boxes with user-defined composition and density.
• Force-field automation – Build OPLS-AA force fields from LigParGen, RESP-fitted, or curated database parameters via PEMD.core.forcefields.Forcefield. Partial charges can be replaced with RESP charges obtained from PEMD's QM pipeline.
• Quantum-chemistry workflows – Perform conformer searches, XTB refinement, Gaussian single-point or optimization jobs, and RESP charge fitting through the PEMD.core.run.QMRun helpers and companion shell scripts.
• MD production runs – Launch annealing and production simulations (GROMACS) with consistent inputs through PEMD.core.run.MDRun using only the JSON specification of system composition.
• High-throughput orchestration – Reusable workflow templates (see workflow/) chain together structure building, parameterization, QM, and MD steps for large screening campaigns.
• Analysis suite – Property analysis modules (e.g., conductivity, diffusion, residence time, glass-transition temperature) under PEMD.analysis accelerate post-processing of simulation trajectories.

Repository Structure

PEMD_DEV/
├── PEMD/                 # Core Python package (modeling, simulation, analysis)
├── workflow/             # Ready-to-run workflow templates and sample inputs
├── bin/                  # Helper shell utilities (e.g., RESP charge automation)
├── environment.yml       # Conda environment for full-featured installations
├── setup.py              # Package metadata for editable/production installs
└── README.md             # Project overview and instructions

Getting Started

Prerequisites

• Operating system: Linux (tested) or macOS. Windows users are encouraged to work within WSL2.
• Conda or Mamba for environment management.
• External simulation engines and quantum-chemistry tools (GROMACS, Gaussian, Multiwfn, XTB, Packmol) available in your runtime environment if you plan to execute the full workflows.

Installation

1. Clone the repository

   git clone https://github.com/HouGroup/PEMD.git
   cd PEMD

2. Create the recommended environment

   conda env create -f environment.yml
   conda activate pemd

3. Install PEMD in editable mode

   pip install -e .

   Editable installs make it easy to track custom modifications while leveraging the packaged entry points.

Quick Start

Below is a minimal Python example that reproduces the molecular-dynamics pipeline shipped in workflow/md.py. It expects a PEMD-style JSON input (see workflow/md.json) describing the polymer chain, salts, and ion counts.

from pathlib import Path
import shutil

from PEMD.core.model import PEMDModel
from PEMD.core.forcefields import Forcefield
from PEMD.core.run import MDRun

work_dir = Path("./demo_md")
work_dir.mkdir(exist_ok=True)

# Copy the example JSON or replace it with your own specification
shutil.copy("workflow/md.json", work_dir / "md.json")
json_file = "md.json"

# 1) Build polymer chains (short + long for charge fitting / production)
pdb_short, pdb_long = PEMDModel.homopolymer_from_json(work_dir, json_file)

# 2) Generate force-field files (LigParGen by default)
Forcefield.oplsaa_from_json(
    work_dir,
    json_file,
    mol_type="polymer",
    ff_source="ligpargen",
    pdb_file=pdb_long,
)
Forcefield.oplsaa_from_json(work_dir, json_file, mol_type="Li_cation", ff_source="database")
Forcefield.oplsaa_from_json(work_dir, json_file, mol_type="salt_anion", ff_source="database")

# 3) Pack the amorphous simulation box and run MD
PEMDModel.amorphous_cell_from_json(
    work_dir,
    json_file,
    density=0.8,
    add_length=25,
    packinp_name="pack.inp",
    packpdb_name="pack_cell.pdb",
)
MDRun.annealing_from_json(
    work_dir,
    json_file,
    temperature=298,
    T_high_increase=300,
    anneal_rate=0.05,
    anneal_npoints=5,
    packmol_pdb="pack_cell.pdb",
)
MDRun.production_from_json(work_dir, json_file, temperature=298, nstep_ns=200)

After the run completes, simulation outputs (topologies, trajectories, logs) reside under the working directory and can be analyzed with the PEMD.analysis modules.

Workflows

The workflow/ directory provides end-to-end templates that can be executed directly or adapted to your project:

Script	Purpose
workflow/md.py	Full MD pipeline: polymer build → force field → annealing → production.
workflow/md_withRESP.py	MD pipeline including RESP charge derivation from QM calculations.
workflow/esw.py	Compute electrochemical stability windows.
workflow/frontier_orbitals.py	Analyze frontier orbitals for small molecules or polymer fragments.

Each script assumes the presence of a PEMD-compatible JSON file (see workflow/md.json) and the necessary external executables in PATH. Treat them as well-documented starting points for your own automation.

Analysis Toolkit

Modules under PEMD.analysis implement commonly used observables for polymer electrolytes:

• conductivity.py, transfer_number.py – Ionic conductivity and transport number calculations.
• msd.py, polymer_ion_dynamics.py, residence_time.py – Mean-squared displacement and ion residence time metrics.
• coordination.py, energy.py, tg.py – Coordination statistics, energetic analyses, and glass-transition estimates.

These utilities consume standard MD trajectories (e.g., XTC, DCD) and topology files. Consult in-code docstrings for details about expected input formats.

Contact

For questions, feature requests, or collaboration opportunities, please contact the PEMD development team at [tsd23@mails.tsinghua.edu.cn].

Citation

If this work is helpful for your research, please cite our paper.

@article{tan2026pemd,
  title   = {PEMD: An open-source framework for high-throughput simulation and analysis of polymer electrolytes},
  author  = {Tan, Shendong and Liang, Bochun and Lu, Dexin and Ji, Chaoyuan and Jia, Wenke and Li, Zihui and Hou, Tingzheng},
  journal = {Digital Discovery},
  year    = {2026},
  DOI     = {10.1039/D5DD00454C},
}