Questions on Non-equilibrium TI Phase with Slurm Scheduler in 'AZtutorial.py' Script

pmx
1

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.

  1. 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?
  2. 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?
  3. 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?
  4. 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?

Thank you!

2

Hi,

  1. I think the tutorial is older, the slurm argument was probably added later and included in the pmx distribution
  2. I haven’t tried this, but please go ahead and test (and report back)
  3. the calculations should be independent so the results should not be affected. sanity-checking is always a good idea, though. So if you see any differences, please report back.
  4. no, this is not necessary, as the dH/dl is computed only for the relevant involved particles. So as long as the systems are “large enough”, there is no need for the bound and unbound states to be identical

Bert