Getting Started with MolPlay

How to Use MolPlay: A Detailed Walkthrough

System Requirements

Before you begin, ensure your system meets the following requirements:

  • CPU: 64-bit x86_64 processor (recommended)
  • RAM: 1 GB minimum, 2 GB or more recommended
  • Graphics Card: Compatible GPU required
    • Refer to the GPU compatibility table in the documentation
    • Integrated graphics may work but dedicated GPUs are preferred for better performance
  • USB Port: Available USB port for the bootable drive
  • BIOS: Ability to boot from USB (may require changing boot order in BIOS settings)

Installation

Overview

  1. Download the MolPlay ISO image from the Download page
  2. Create a bootable USB stick using the ISO image. You need at least a 16 GB USB stick. Use software like Rufus or Etcher
  3. Boot your computer from the MolPlay USB stick

Downloading MolPlay

  1. Navigate to the Download page on the MolPlay website
  2. Locate the latest version of the MolPlay ISO image
  3. Click the download link and save the ISO file to your computer
  4. Verify the download by checking the MD5 checksum

Creating a Bootable USB Drive

You’ll need a USB drive with at least 16 GB capacity. Warning: This process will erase all data on the USB drive.

  • Using Rufus (Windows):
    1. Download and install Rufus from https://rufus.ie/
    2. Insert your USB drive
    3. Open Rufus
    4. In Rufus, select your USB drive in the “Device” dropdown
    5. Click “SELECT” and choose the MolPlay ISO file that you downloaded
    6. Click “Start” and wait for the process to complete
  • Using Etcher (Windows, macOS, Linux):
    1. Download and install Etcher from https://www.balena.io/etcher/
    2. Insert your USB drive
    3. Open Etcher
    4. Click “Flash from file” and select the MolPlay ISO you downloaded
    5. Click “Select target” and choose your USB drive
    6. Click “Flash!” and wait for the process to complete
  • Note on USB Drive Partition Size

    By default, MolPlay creates a fixed-size partition designed for 16 GB USB drives. If your USB drive is larger, you can enable automatic resizing to utilize the full capacity:

    Option 1: Edit before booting

    1. After creating the bootable USB, mount it on a Mac/Windows/Linux system
    2. Locate and edit the file `/boot/batocera-boot.conf`
    3. Find the line `#autoresize=true` and uncomment it (remove the `#`)
    4. Save the file and safely eject the USB drive

    Option 2: Edit after booting MolPlay

    1. Boot into MolPlay
    2. Open a terminal (press F1)
    3. Run the following commands:

    #+begin_src shell ystem Requirements

    Before you begin, ensure your system meets the following requirements:

    • CPU: 64-bit x86_64 processor (recommended)
    • RAM: 1 GB minimum, 2 GB or more recommended
    • Graphics Card: Compatible GPU required
      • Refer to the GPU compatibility table in the documentation
      • Integrated graphics may work but dedicated GPUs are preferred for better performance
    • USB Port: Available USB port for the bootable drive
    • BIOS: Ability to boot from USB (may require changing boot order in BIOS settings)

Installation

Overview

  1. Download the MolPlay ISO image from the Download page
  2. Create a bootable USB stick using the ISO image. You need at least a 16 GB USB stick. Use software like Rufus or Etcher
  3. Boot your computer from the MolPlay USB stick

Downloading MolPlay

  1. Navigate to the Download page on the MolPlay website
  2. Locate the latest version of the MolPlay ISO image
  3. Click the download link and save the ISO file to your computer
  4. Verify the download by checking the MD5 checksum

Creating a Bootable USB Drive

You’ll need a USB drive with at least 16 GB capacity. Warning: This process will erase all data on the USB drive.

  • Using Rufus (Windows):
    1. Download and install Rufus from https://rufus.ie/
    2. Insert your USB drive
    3. Open Rufus
    4. In Rufus, select your USB drive in the “Device” dropdown
    5. Click “SELECT” and choose the MolPlay ISO file that you downloaded
    6. Click “Start” and wait for the process to complete
  • Using Etcher (Windows, macOS, Linux):
    1. Download and install Etcher from https://www.balena.io/etcher/
    2. Insert your USB drive
    3. Open Etcher
    4. Click “Flash from file” and select the MolPlay ISO you downloaded
    5. Click “Select target” and choose your USB drive
    6. Click “Flash!” and wait for the process to complete
  • Note on USB Drive Partition Size

    By default, MolPlay creates a fixed-size partition designed for 16 GB USB drives. If your USB drive is larger, you can enable automatic resizing to utilize the full capacity:

    Option 1: Edit before booting

    1. After creating the bootable USB, mount it on a Mac/Windows/Linux system
    2. Locate and edit the file `/boot/batocera-boot.conf`
    3. Find the line `#autoresize=true` and uncomment it (remove the `#`)
    4. Save the file and safely eject the USB drive

    Option 2: Edit after booting MolPlay

    1. Boot into MolPlay
    2. Open a terminal (press F1)
    3. Run the following commands:
    mount -o remount,rw /boot/
nano /boot/batocera-boot.conf
    1. Find the line #autoresize=true and uncomment it (remove the `#`)
    2. Save the file (Ctrl+X, then Y, then Enter)
    3. Reboot the system

    After enabling autoresize and rebooting, MolPlay will automatically expand to use the full capacity of your USB drive.

Booting from the MolPlay USB

  1. Insert the MolPlay USB drive into your computer
  2. Restart your computer
  3. During startup, press the key to enter the boot menu (often F12, F2, or Del - check your computer’s manual).
  4. In the boot menu, select the USB drive as the boot device. If it does not show up, you may need to switch between legacy and UEFI boot modes, depending on your computer.
  5. Your computer should now boot into MolPlay

If you encounter issues booting, consult the troubleshooting guide or drop us an email.

Navigating the MolPlay Interface

Overview

  1. Use the Emulation Station menu to browse available examples
  2. Check available instructions on-screen for each experiment
  3. Select an example to launch the interactive simulation

Menu navigation: launching your first simulation

Once MolPlay has booted successfully, you’ll see the Emulation Station interface. Right now there is a single collection of examples available. There is also background music playing.

  1. From the main collection, use the Enter key to see all available examples
  2. Use Up / Down arrow keys to browse available simulations
    • There is an image and a brief description for each example; the description is read by a synthetic computer voice every time a new line is selected
    • Use a long press on Enter to bring up the extended menu for the selected example. This feature gives you access to a written manual by choosing View Game Manual or to an image by choosing View Game Media
    • Press Enter to launch the selected simulation
  3. Press Esc to go back from the example submenu to the main menu
  • Setup and configuration:

    The general Batocera Linux and EmulationStation functionalities are accessible. You can for instance access the EmulationStation main menu using the spacebar key. An overview is given in the Batocera wiki page on EmulationStation. You should also consult this wiki if you have any trouble or are looking for assistance with setup, for instance to make audio work or configure network accessibility.

    • Documentation: View the user manual using the Quick Access menu via the backspace key in the main menu (not the “game” submenu)
    • Settings: Adjust system and display settings using the EmulationStation main menu described above

Interacting with Simulations

Each simulation may have slightly different controls, but generally:

  • Mouse, left-click and drag in the void: Rotate the view
  • Left-click and drag on an atom: Apply forces to molecules
  • MIddle-click and drag: pan the view
  • Right-click and drag: Zoom in/out
  • Scroll wheel: Zoom in/out
  • Ctrl + X: Exit the simulation and return to the menu

Refer to the instructions or documentation for simulation-specific controls.

Exploring MolPlay

Tips for Beginners

  • Start with simpler examples like “Deca-alanine helix in water” before moving to more complex systems
  • Take time to read the documentation for each example before launching
  • Experiment with different interactions and observe how the system responds
  • Don’t hesitate to restart a simulation if you want to try a different approach

A description for the examples is provided here.

Exploring More Examples

As you become comfortable with basic simulations, explore more complex examples:

  1. Return to the main menu by pressing Ctrl + X when in a simulation
  2. You may also go back to the Main menu via Esc and/or re-select “Examples” with Enter
  3. Browse through more advanced simulations like “VAMP-CG-v1” or “FepA iron transporter”
  4. Challenge yourself with different molecular systems and interaction scenarios

Accessing Help and Documentation

If you need additional assistance:

  1. From the main menu, select “Documentation”
  2. Browse through available topics for detailed information
  3. Look for video tutorials that may be available for specific examples
  4. Check our Frequently Asked Questions (F.A.Q.) section
  5. Ask our (experimental) Chatbot

If you do get stuck, do not panic! You can always drop us an email.

Remember, practice and experimentation are key to mastering interactive molecular simulations with MolPlay!

Explore MolPlay examples