bstates and common files in DL-WESTPA

[Megha Parashar]

Hello all,

I am quite new to WESTPA and trying to understand different variations of it. While brushing through the input files of DL-WESTPA I noticed that the bstates.txt files are different in DL-WESTPA as compared to other variants of it. Why is that so?
What exactly is the file pattern followed in DL-WESTPA?

Also, since the files provided here are for the synMD simulation, I could not understand which files are critical/and required to run the DL-WESTPA simulation with real simulations? And, why are there two west.cfg files here (there's one present in common files folder as well)?

Thanks,

Megha

[Jeremy Leung]

Hi Megha,

Welcome to the community!

1. The `bstates/` files are a little different for `DL-enhancedWE` (missing folders/files for each bstate) because SynD only requires the state number/cluster number (third column in bstates.txt) to represent where the segment is (i.e. the cluster number is equivalent to a restart file). If you're not doing synd, then the structure would be much more like all the examples in westpa/tutorials, where the third column would point to the folder of the bstate or directly at the restart files.

2. Likewise, the `west.cfg` file in `common_files` is just a leftover for running synd in a WE simulation without DL. Safe to ignore. Running DL-enhancedWE, your west.cfg would follow very much like the one in the root directory. You would probably have to remove/modify the section in west.propagation (https://github.com/westpa/DL-enhancedWE/blob/main/west.cfg#L116-L119) and parameters for training. All the propagation bits (i.e. what's typically in westpa_scripts) are all bundled up in a specific class in the synd package, which is why the file structure is simplified.

3. To not run synd using that set up, I would actually start with one of the westpa/tutorials setup, and copy west.cfg (from root) and the `deepdrivewe` folder . If you are using a static model, also copy/move equivalent files as the static_model, scripts folder as well. Modify what's in westpa_scripts (and potentially in the deepdrivewe folder) to extract features to run training/inference (i.e. match what's equivalent in the augmentation driver https://github.com/westpa/DL-enhancedWE/blob/main/common_files/augmentation_driver.py).

-- JL

---
Jeremy M. G. Leung, PhD
Research Assistant Professor, Chemistry (Chong Lab)
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml...@pitt.edu | [He, Him, His]