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Revision as of 16:18, 16 May 2011
Recent events
What is Alchemistry?
Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate the free energies of various physical processes, such as the free energy of ligand binding to a macromolecular receptor, or the transfer of a small molecule from gas to water. The alchemistry.org logo graphic above depicts such an example, where the free energy of ligand binding to a protein receptor is computed by computationally simulating alchemical intermediates with weakened interactions with the rest of the system. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant physical contributions to binding affinity.
What is here?
In these pages, we will provide information about these alchemical free energy calculations. This information falls into several categories, and some are is still to be prepared.
Things that are now here:
- Best Practices: Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work.
- Gromacs Tutorials: A set of tutorials for conducting several specific alchemical free energy calculations with the GROMACS simulation package, to allow beginners to get their feet wet.
- Free Energy References: A publicly editable, categorized list of references with annotations relating to free energy calculations, so you can stay abreast of the latest literature, add links to your own work, and comment. The reference database is currently being transitioned to a Zotero group, web accessible here, but much more fully featured downloading the Zotero plug in. Please contact Michael Shirts (michael.shirts at virginia.edu) for more editable access.
- Free Energy Tools: Some tools related to free energy calculations. These are somewhat preliminary.
Things that are coming:
- Test System Repository: A repository of standard test systems (including parameters, preferably in multiple formats) for alchemical free energy calculations, along with known results with those parameters, and benchmark test sets.
- Free Energy Introduction: An introduction to free energy calculations generally, with a slant towards alchemical methods. Hopefully this will provide a good starting point for students beginning work in the area, and will be suitable for advanced undergraduate or early graduate students.
Please be warned that, as this is a new page (and a Wiki), this information is in a state of flux.
Who runs Alchemistry?
About the Wiki
- Why do we need an Alchemistry wiki? Why Alchemistry.org?
- How You Can Help.
Using MediaWiki
- Wikitext markup examples
- Consult the User's Guide for information on using the wiki software.
- Configuration settings list
- MediaWiki FAQ
- MediaWiki release mailing list