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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

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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!)

Once you join the group, adding new articles is easy with the | Cite-u-Like bookmarklet

Events: Conferences relating to free energy methods.

Example Free Energy Calculations

A look into practical examples without software-specific details. We outline the steps needed for realistic free energy problem, detailing problems you can expect to encounter, and how to analyze the data to get a robust 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.

Job postings

Job postings in computational chemistry and alchemical free energy calculations.

RSS feed of recent papers added to the database

All these papers have been linked through the CiteULike group. Abstracts can be accessed by the link in the section title. Get the RSS.

Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites

— Michael Shirts — Date Added: 2015-02-21 21:08:08

On the Efficiency of Exchange in Parallel Tempering Monte Carlo Simulations

— Cristian Ciobanu — Date Added: 2015-02-21 20:45:44

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

— Michael Shirts — Date Added: 2015-02-21 20:39:47

Practical Aspects of Free-Energy Calculations: A Review

— Wilfred van Gunsteren — Date Added: 2014-05-25 02:33:50

Accuracy Assessment and Automation of Free Energy Calculations for Drug Design

— Thomas Fox — Date Added: 2013-11-27 21:33:55

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