Difference between revisions of "Example Free Energy Calculations"
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| − | =[[Example: Binding to T4-Lysozyme|Binding Free Energy Examples]]= | + | =[[Example: Binding to T4-Lysozyme| 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. | Go through the setup up and define the thermodynamic cycle for transforming one molecule to another within a binding pocket. | ||
{| | {| | ||
| − | | [[File:T4-Toluene.png|thumb| | + | | [[File:T4-Toluene.png|thumb|300px|Toluene in the pocket...]] |
| [[file:Doublearrow.png|100px]] | | [[file:Doublearrow.png|100px]] | ||
| − | | [[File:T4-Phenol.png|thumb| | + | | [[File:T4-Phenol.png|thumb|300px|... becomes phenol in the pocket.]] |
| + | |} | ||
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| + | =[[Example: Absolute Binding Affinity| Absolute Binding Affinity Example]]= | ||
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| + | Apply everything together to do one of the harder but very common free energy calculations of an absolute binding affinity. | ||
| + | {| | ||
| + | | [[File:T4-Tol-Imp.png|thumb|200px|Toluene in the complex system...]] | ||
| + | | [[file:Doublearrow.png|50px]] | ||
| + | | [[File:T4-Imp.png|thumb|200px|...an unbound system...]] | ||
| + | | [[File:Plus_sign.jpg|50px]] | ||
| + | | [[File:Tol-Imp.png|thumb|100px|...and a free toluene in solution.]] | ||
|} | |} | ||
Revision as of 08:18, 4 January 2013
| Free Energy Fundamentals |
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Methods of Free Energy Simulations
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| Free Energy How-to's |
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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.
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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.
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Absolute Binding Affinity Example
Apply everything together to do one of the harder but very common free energy calculations of an absolute binding affinity.
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