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Introduction
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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.
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MD Simulation of Alkanes
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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).
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MD Simulation of a Protein
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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.
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Git and GitHub
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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.
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Putting It All Together
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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.
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