Molecular Mechanics Tools: Glossary

Key Points

  • Molecular mechanics simulations use classical physics to calculate properties of molecules and materials

  • A force field is an equation describing the potential energy of a system.

  • Force fields have terms for bonds, angles, dihedrals (bonded terms), and Van der Waals and electrostatic (nonbonded) interactions.

  • We are going to use a software called OpenMM to simulate our molecules.

  • OpenMM understands force fields in a format called an XML file.

MD Simulation of Alkanes
  • Typical MD simulations consist of simulation initialization, minimization, equilibration, and production.

  • The production simulation gives the data which is analyzed.

  • Results from simulation can be used to calculate the potential of mean force (PMF).

MD Simulation of a Protein
  • Preparing a protein for an MD simulation has several steps. You will often use existing tools to help with this task.

  • Identifying the relevant bond lengths and angles to analyze and graph is an important part of analyzing a molecular dynamics simulation.

  • Landmark simulations from the early days of molecular dynamics can now be completed in a few minutes on modern laptops.

Git and GitHub
  • Version control keeps a complete, organized history of all work on a project. It is extremely useful whether you are working individually or on a team.

  • Good commit messages are critical to maintaining an organized and useful repository.

  • Putting your code on GitHub is the best way to easily share your code, collaborate, and track changes.

Putting It All Together
  • Large coding projects often have hundreds, if not thousands of developers working togehter on code. Using version control can help many people implement new features at once.

  • Use online documentation from coding projects to learn about existing functions and features when you are trying to change existing code.

  • When you write new code, always document your functions so that other people will be able to understand and build on your work.