Polymer MD Workshop

This workshop is organized in collaboration with MetaChem Academy.

Recording Playlist: YouTube Workshop Recordings

#> All session recordings will appear at this playlist after the workshop is finished. The videos are non-downloadable and will remain available for 1 year.

Resources Folder: Google Drive Resources

This repository contains Jupyter notebooks and scripts for a hands-on workshop on molecular dynamics (MD) simulations of polymers using AmberTools and GROMACS. The workshop is organized into several days, each focusing on a key aspect of polymer simulation, from small molecule parameterization to full MD production and analysis.

Enjoy the workshop and happy simulating!

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Quick Install & Initial Steps

Initial Setup (Run Only Once)

1. Clone or Download the Repository:

git clone https://github.com/hargu978/polymermd-workshop.git
cd polymermd-workshop

Or download and unzip from GitHub if you prefer.

2. Set Up the Conda Environment:

chmod +x setup_conda_env.sh
./setup_conda_env.sh

This script will install Miniconda (if needed), create the polymer_md environment, and install all required packages (AmberTools, GROMACS, nglview, etc.).

Note: Steps 1 and 2 only need to be run once per machine or when you want to update/reset the environment.

Every New Session (Run Every Time You Start Work)

3. Open a Terminal and Navigate to the Workshop Folder:

• On Windows, open your Ubuntu (WSL) terminal.
• On Linux/MacOS, open your regular terminal.
• Navigate to the workshop folder (replace PATH_TO with your actual path):

  cd PATH_TO/polymermd-workshop

4. Activate the Environment:

conda activate polymer_md
source $CONDA_PREFIX/amber.sh

5. Start Jupyter Lab:

jupyter lab --ip 0.0.0.0 --no-browser

Open the URL printed in the terminal to access the notebooks in your browser.

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Workshop Structure & Notebook Overview

The workshop is organized by day, with each day having a dedicated Jupyter notebook in the Day1,2-Ambertools-solved/, Day3-gen-polymer-solved/, and Day4,5-gmx-md-simulation-analysis/ folders. Below is a summary of what is covered each day:

Related Markdown Documentation:

• Conda Setup Guide (step-by-step)
• Polymer parameterization and chain building (Day 3)
• GROMACS system preparation and equilibration (Day 4)
• GROMACS production and analysis (Day 5)

Day 1: Small Molecule Parameterization with AmberTools

• Notebook: Day1_ambertools_tutorial.ipynb
• Folder: Day1,2-Ambertools-solved/
• Topics:
  • Converting SMILES to 3D structures (OpenBabel)
  • Assigning GAFF atom types and AM1-BCC charges (antechamber)
  • Generating missing force field terms (parmchk2)
  • Building topology and coordinate files (tleap)
  • Example: Ethanol parameterization and topology generation

Day 2: Polymer Monomer Parameterization

• Notebook: Day1_ambertools_tutorial.ipynb (continued)
• Folder: Day1,2-Ambertools-solved/monomer/
• Topics:
  • Parameterizing polymer monomers (PEO, PET)
  • Generating force field files for monomers
  • Preparing for polymer chain construction

Day 3: Polymer Chain Construction

• Notebook: Day3_generate_polymerchains_tutorial copy.ipynb
• Folder: Day3-gen-polymer-solved/
• Topics:
  • Building polymer chains from monomer units
  • Generating random and block copolymers (PEO/PET)
  • Creating GROMACS-compatible topology and coordinate files for polymers

Day 4: System Preparation & Equilibration with GROMACS

• Notebook: Day4_gromacs_formats_tutorial.ipynb
• Folder: Day4,5-gmx-md-simulation-analysis/
• Topics:
  • Setting up the simulation box and solvating the polymer
  • Adding ions for neutralization
  • Energy minimization and stepwise equilibration (NVT, NPT)
  • Editing topology files for solvent/ions
  • Extracting and visualizing energy terms (temperature, density)

Day 5: Production MD & Analysis

• Notebook: Day5_gmx_prod_analysis_tutorial.ipynb
• Folder: Day4,5-gmx-md-simulation-analysis/
• Topics:
  • Running production MD simulations (5–10 ns)
  • Analyzing trajectories: RMSD, radius of gyration, RDFs
  • Glass transition temperature analysis via simulated annealing
  • Visualization with nglview, MDAnalysis, matplotlib
  • Example SLURM scripts for HPC job submission

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Additional Notes

• All notebooks are designed to be run interactively in Jupyter Lab after activating the polymer_md environment.
• Example input/output files are provided in the relevant folders for each day.
• For troubleshooting or manual installation, see the environment.yml and setup_conda_env.sh scripts.
• Install WSL Ubuntu (for Windows users)
• For more details on Jupyter, see:
  • Jupyter Notebook Basics
  • Jupyter Lab Interface

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Workshop Author:

Harish Gudla
Computational Material Scientist, Compular, Sweden
LinkedIn: Harish Gudla

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License

This tutorial is provided under the MIT License. Use it freely for educational and research purposes.