This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
1) I reworked very minimally the submission system to do two things:
-Check for nans in the output cnf/trc files from simulation to avoid crashes mid-run. This is a temporary fix before we figure out how to change the gromos code.
-Wrote the input in the .sh scripts which call the repex_mpi for the calculations
such that input would be more human readable.
-Removed copy statements which are now unnecessary in these same .sh scripts
-Tweaked the path that of the coordinates which are written to schedule_production_jobs.py (note: I might have to do something similar for the energy offset and sopt submission).
2) Included a new plot which calculates the sampling of end states (and their evolution in time) for a simulation. Note that this code is not called anywhere, as I am currently just using it from a jupyter notebook. But it could be included in the analysis of s-opt and production runs in the future.
What would be very helpful would be to run energy offset runs, and s-opt runs to ensure that the paths to the imds/cnfs are all good.
Description
There are two tings in this pull request:
1) I reworked very minimally the submission system to do two things:
-Check for nans in the output cnf/trc files from simulation to avoid crashes mid-run. This is a temporary fix before we figure out how to change the gromos code.
-Wrote the input in the .sh scripts which call the repex_mpi for the calculations such that input would be more human readable.
-Removed copy statements which are now unnecessary in these same .sh scripts
-Tweaked the path that of the coordinates which are written to schedule_production_jobs.py (note: I might have to do something similar for the energy offset and sopt submission).
2) Included a new plot which calculates the sampling of end states (and their evolution in time) for a simulation. Note that this code is not called anywhere, as I am currently just using it from a jupyter notebook. But it could be included in the analysis of s-opt and production runs in the future.
What would be very helpful would be to run energy offset runs, and s-opt runs to ensure that the paths to the imds/cnfs are all good.
Candide