Optimizing FEP Schedules from AR Data#

This recipe shows how to generate a denser SSC(alpha) lambda schedule from existing analysis-ready overlap or replica-exchange data with batter fek-schedule.

Example Command#

batter fek-schedule --opt 48 -o sched.ar.z.dat --plot sched.ar.z.png -T 298.15 --start 0 --stop 8 --ssc --ar /path/to/executions/run-id/simulations/transformations/lig1~lig2/fe/comp/

What This Does#

  • --opt 48 optimizes a fresh schedule with 48 lambda values.

  • --ar targets the predicted replica-exchange ratio.

  • --ssc restricts the search to SSC(alpha) schedules.

  • -o sched.ar.z.dat writes the optimized schedule to disk.

  • --plot sched.ar.z.png writes the corresponding heatmap/path projection plot.

  • -T 298.15 sets the temperature in Kelvin.

  • --start 0 --stop 8 trims the data range passed into the scheduling utility.

Input Directory#

Point the final positional argument at the component folder containing the FE analysis data. For RBFE transformations this is typically the x component, for example:

/path/to/executions/run-id/simulations/transformations/lig1~lig2/fe/x/

If you use a placeholder such as comp in scripts or notes, replace it with the actual component directory before running the command.