Examples

Here are some examples on how to use the pmx library to carry out the key steps in the setup and analysis of alchemical free energy calculations. Using the API is useful if you want to automate the setup for many calculations.

• Create Mutant Structure
• Generate Hybrid Topology
• Analyse Results

Another way to setup the files needed for the calculations is via the command line tools, which may be more convenient to use for a small number of calculations.