Main Page

---

What is Alchemistry?

Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate the free energies of various physical processes. Such process include ligand binding to a protein receptor, the transfer of a small molecule from gas to water, or the free energy of a mutation of a side chain. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant interactions driving binding.

Getting Started with Free Energy Methods

This site is designed to both give novices best practices information about how to perform free energy calculations, and to provide an ongoing reference for the current state of research into methods for calculating free energies.

Free Energy Fundamentals Learn the methods and techniques behind free energy methods with in-depth coverage of free energy definitions and topics. Best Practices in Free Energy Methods Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work. Free Energy References An 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 database is implemented as a CiteULike group, with over 700 articles. And probably there are another 700 that we should have up, so please join and add your favorite papers (especially your own work!) Events: Conferences relating to free energy methods.

Example Free Energy Calculations A look into practical examples without software-specific details. Here you will see the steps needed in a real free energy problem, what problems you can expect to encounter, and how to analyze the data to get a free energy difference. Tutorials and How-to's Tutorials for conducting several specific alchemical free energy calculations with a variety of simulation packages, to allow beginners to get their feet wet. These guides will walk you through setting up software-specific free energy simulations and their analysis. Test System Repository A repository of standard test systems (including parameters, often in multiple file formats) for alchemical free energy calculations, along with known results with those parameters, and benchmark test sets..

RSS feed of recent papers added to the Alchemistry.org database

All these papers have been linked through the Alchemistry.org CiteULike group. Abstracts can be accessed by the link in the section title. Get the RSS. Failed to load RSS feed from http://www.citeulike.org/rss/group/14929: There was a problem during the HTTP request: 403 Forbidden

About the Alchemistry.org wiki

Who runs Alchemistry.org?

• Read About the Editors

Contributing to Alchemistry.org

• How You Can Help. Add your own experience to what is posted here!

Using MediaWiki in Alchemistry.org

• Creating citations on Alchemistry.org
• Wikitext markup examples
• Consult the User's Guide for information on using the wiki software.
• Configuration settings list
• MediaWiki FAQ
• MediaWiki release mailing list