GROMACS StepWizard

Struggling to determine the exact number of steps for your GROMACS molecular dynamics simulations? Meet GROMACS StepWizard – a powerful tool that automates step calculations for your desired simulation time in nanoseconds! GROMACS StepWizard is a also a web-based tool designed to help you easily generate production.mdp files for GROMACS simulations. It simplifies the process by allowing you to input desired simulation times and automatically calculates the required parameters.GROMACS StepWizard is a web-based tool designed to help you easily generate production.mdp files for GROMACS simulations. It simplifies the process by allowing you to input desired simulation times and automatically calculates the required parameters.

Access the app here

https://gromacs-stepwizard-7e3791398062.herokuapp.com

Youtube Link: https://www.youtube.com/watch?v=RWzqH28UeLE

Features

• Input simulation time in picoseconds (ps) or nanoseconds (ns).
• Automatically calculates the number of steps (nsteps).
• Generates a production.mdp file for GROMACS.
• Provides detailed information about important parameters like dt, nsteps, etc., through an easy-to-access help page.

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Technologies Used

• Python with Flask framework
• HTML/CSS for the front-end
• Deployed on Heroku

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How to Run the App Locally

Prerequisites

1. Install Python (3.7 or higher).
2. Install pip (comes with Python installation).

Steps

1. Clone the repository:

   git clone https://github.com/your-username/gromacs-stepwizard.git
   cd gromacs-stepwizard

2. Create a virtual environment and activate it:

   python -m venv venv
   source venv/bin/activate  # On Windows: venv\Scripts\activate

3. Install dependencies:

   pip install -r requirements.txt

4. Run the app:

   python app.py

5. Open your browser and navigate to:

   http://127.0.0.1:5000/
   

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How to Deploy to Heroku

Prerequisites

1. Install the Heroku CLI.
2. Sign up for a Heroku account.

Steps

1. Log in to Heroku:

   heroku login

2. Create a new Heroku app:

   heroku create your-app-name

3. Push the code to Heroku:

   git push heroku main

4. Open your app:

   heroku open

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File Structure

project-folder/
│
├── app.py              # Main application file
├── requirements.txt    # Dependencies for the app
├── Procfile            # Heroku configuration file
├── runtime.txt         # (Optional) Specifies Python version
├── templates/          # HTML templates for the app
│   ├── index.html      # Main input page
│   ├── result.html     # Results display page
│   ├── info.html       # Help page for parameters
├── static/             # (Optional) Contains CSS/JS files
│   ├── style.css       # Styling for the app
└── production_files/   # Folder to store generated .mdp files

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Screenshots

Main Page

Results Page

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Author

Pritam Kumar Panda
Stanford University
GitHub | LinkedIn

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License

This project is licensed under the Apache License 2.0. See the LICENSE.txt file for details.