Hello PMX community,
I have been using a customized ‘AZtutorial.py’ script from the tutorial, and I’ve come across a few questions related to non-equilibrium TI phase calculations with the Slurm scheduler.
- Absence of Slurm’s Array Argument in ‘AZtutorial.py’ Script: I noticed that there is no slurm’s array argument in the
_submission_script()method inside the ‘AZtutorial.py’ script. However, in the ‘jobscript.py’ script within pxm’s src, there is an slurm array argument in the
_submission_script()method. Was the exclusion of the array in ‘AZtutorial.py’ intentional, perhaps for tutorial simplicity?
- Performance Increase with Slurm Array: I am interested in utilizing Slurm’s array feature using the
_submission_script()method from the ‘jobscript.py’ script in pxm’s src. It seems that using an array could lead to a significant performance increase. Have others in the community experimented with this, and if so, what were the outcomes?
- Differences in Results or TI Calculations with Array: When using Slurm’s array, do the results differ from those obtained using a for loop? Are there any considerations or potential issues that one should be aware of when employing the array feature, especially concerning the calculation of non-equilibrium TI?
- System Size Consistency for Unbound and Bound States: In the context of using non-equilibrium transitions between the unbound state and the bound state (complex), is it necessary for the system sizes to be the same when creating the two-state boxes? Does maintaining equal system sizes play a crucial role in achieving accurate results for such transitions?