Example Free Energy Calculations

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Even with the most detailed and clear description of a problem and how to solve it, it is always good to see how to put that description into practice. The examples shown here are only simple examples, but they do outline and cover the basics which were described above. It should be noted that these examples do not walk you through actually simulating a system, but instead guide you through the decision process you would follow to run your simulation. There is an excellent free energy walkthrough for GROMACS written by Justin Lemkul of Virginia Tech available if you would like specific instructions for a free energy simulation.

Please consult any of the examples below to see how to go about setting up your free energy calculation:

Solvation Free Energy Example

Learn about the free energy of solvating a molecule into water.

Transform a system from a simple water box...
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... to a system with a molecule present.

Relative Binding Free Energy Examples

Go through the setup up and define the thermodynamic cycle for transforming one molecule to another within a binding pocket.

Toluene in the pocket...
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... becomes phenol in the pocket.

Absolute Binding Affinity Example

Apply everything together to do one of the harder but very common free energy calculations of an absolute binding affinity.

Toluene in the complex system...
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...an unbound system...
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...and a free toluene in solution.