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NMR Meets Biology: Numerical Simulations from First Principles

📖 How to Use This Tutorial

There are approximately 16 problems designed to simulate specific aspects of spin dynamics, share as Jupyter notebooks. Each notebook starts with a setup that has some code that will help you get started on the main aspects of the problem. It is then followed one or more questions as a follow-up that you will need to solve.

The first two sections: 'Basis' and 'Evolution' essential. The results from these notebooks can be turned into convenience functions that will greatly simplify the code for all other notebooks. The code to be copied is given at the end. You can turn your notebook cells into functions by manually copying them into a python ('.py') file which is kept in the same folder.

If you do not know anything about Python, the prerequisites section gives you a crash course on the required elements. This should not be done during the tutorial. You should instead pair up with someone who knows a bit of Python and follow along.

Some 'real' NMR simulation software

  1. SIMPSON
  2. GAMMA
  3. SPINACH
  4. SpinEvolution
  5. Spindynamica
  6. ChemEx
  7. SLEEPY

Resources

  1. Hodgkinson, P., and Emsley, L. (2000) Numerical simulation of solid-state NMR experiments. Prog. Nucl. Magn. Reson. Spectrosc., 36 (3), 201–239.
  2. Edén, M. (2003) Computer simulations in solid-state NMR. I. Spin dynamics theory. Concepts Magn. Reso. A, 17 (1), 117–154.
  3. Edén, M. (2003) Computer simulations in solid-state NMR. II. Implementations for static and rotating samples. Concepts Magn. Reso. A, 18 (1), 1–23.
  4. Edén, M. (2003) Computer simulations in solid-state NMR. III. Powder averaging. Concepts Magn. Reso. A, 18 (1), 24–55.
  5. Mueller, L.J. (2011) Tensors and rotations in NMR. Concepts Magn. Reson. Part A, 38 A (5), 221–235.