Scripts for running alchemical free-energy perturbation simulations using Gromacs.
Allows specification of host/queue and contains commands to prepare and submit simulations.
Contains all information for writing batch files to be submitted to the queue.
Copies all dhdl.xvg files into the respective mbar_analysis folder for each thermodynamic leg and runs mbar calculations on it from the alchemical-analysis repository. The resulting free energies are organized into a plottable output file with error bars, and the overall energies are also reported.
Shows how the results converge when removing the first 1-15 picoseconds of simulation. (This one will take a few hours).