6. More Notes !!

Notes I wish I had showed me when I started

This collection was an attempt to consolidated my experiences in computational chemistry. Entering the field with no background in mathematics or computers, a lot was learned through trial and error. Despite these shortcomings, I am forever grateful to the exceptional guidance and continued support of Dr. Genwei Zhang, Dr. Zheng Pei, Dr. Xiaoliang Pan, and Dr. Yihan Shao.

I hope many of you will find this information useful in your future endeavors.

• 6.1. Compile Notes
• 6.2. apptainer
  • 6.2.1. apptainer build
  • 6.2.2. apptainer run
  • 6.2.3. apptainer shell
  • 6.2.4. apptainer instance start
    • 6.2.4.1. Instances
• 6.3. Apptainer
  • 6.3.1. Build
  • 6.3.2. Run
• 6.4. ChimeraX
• 6.5. ffmpeg: Movies
  • 6.5.1. Convert ppm to png
• 6.6. GNU Parallel
  • 6.6.1. Running Parallel on HPCs
  • 6.6.2. Parallel Umbrella Sampling Windows for MD Simulations
• 6.7. How to install AutoDock-GPU on Apple silicon
  • 6.7.1. 1. Install Homebrew if needed
  • 6.7.2. 2. Install the required OpenMP runtime
  • 6.7.3. 3. Download the Apple Silicon AutoDock-GPU binary
  • 6.7.4. 4. Create a program directory for AutoDock-GPU
  • 6.7.5. 5. Move the downloaded binary into place
  • 6.7.6. 6. Create a convenient command-line symlink
  • 6.7.7. 7. Add $HOME/Programs/bin to your PATH
  • 6.7.8. 8. Test the installation
  • 6.7.9. 9. Example run command
  • 6.7.10. 10. Troubleshooting
    • 6.7.10.1. Error: Library not loaded: /opt/homebrew/opt/llvm/lib/libomp.dylib
    • 6.7.10.2. Error: permission denied
    • 6.7.10.3. Error: macOS says the file cannot be opened
    • 6.7.10.4. Check what libraries the binary needs
  • 6.7.11. Final installed layout