May 15, 2016 · Job postings in computational chemistry and alchemical free energy calculations. RSS feed of recent papers added to the Alchemistry.org database. All these papers have been …

Jul 10, 2013 · Why the name "Alchemical"? One of the first questions, and often most confusing points, about a number of free energy calculations is why we refer to them as "alchemical" …

Mar 19, 2015 · The Bennett Acceptance Ratio (BAR) is one of the earliest free energy methods which draws on data from multiple states to estimate the free energy difference; This method …

Jul 17, 2013 · The Weighted Histogram Analysis Method (WHAM) is one of the earliest methods that take into account information from all Intermediate States.By analyzing all the information …

Jun 5, 2014 · Setting up the calculation with Gromacs. This tutorial assumes knowledge of Gromacs.Make sure you actually know how to use Gromacs first. There are nine intermediate …

Jun 18, 2013 · This example will be different still from the other two examples in that this will touch on both the pulling method and the alchemical decoupling. Either of these methods are …

The best way to show how efficient thermodynamic paths can make simulations quicker is with an illustrative example shown on the right. The situation is that we wish to find which ligand, A or …

Overview. Many interesting processes involve ions changing chemical environment, such as the transfer of an ion from the gas phase to the solvated phase, the protonation of a protein side …

Mar 23, 2017 · GROMACS Tutorials. A very useful tutorial for calculating free energies in GROMACS 4.5.3 by Justin Lemkul.. For tutorials for 4.6.3 and later versions of GROMACS, …

Aug 12, 2016 · The largest problem with linear scaling is that it gives very unequal phase space overlap between states. This has been a long acknowledged problem with several easily …