Data passing for multiple pcoords

[Shashank Shastry]

Hello westpa-users,

I am trying to implement 2D steady -state westpa trying to capture protein dimer complexes in membranes. Currently, I am running into issues with reading pcoords. Here is what I have tried so far:

- I have tested my pcoord script, no issues outputting data to dist.txt and cangle.txt

- There seem to be no MD related issues, GROMACS runs fine and segment 1 completes with no errors.

- I tinkered a bit with variable naming in the westpa_scripts/runseg.sh file. Perhaps I am doing this step incorrectly?

- I modified the pcoord return line to this:

cat $WEST_CURRENT_SEG_DATA_REF/dist.txt | awk '{print $1;}' > $WEST_DIST_RETURN
cat $WEST_CURRENT_SEG_DATA_REF/cangle.txt | awk '{print $1;}' > $WEST_CANGLE_RETURN

My output log is below:

WESTPA environment activating ...
Updating system with the options from the configuration file
Creating HDF5 file '/raid/.../west.h5'
1 target state(s) present
Calculating progress coordinate values for basis states.
1 basis state(s) present
Calculating progress coordinate values for start states.
0 start state(s) present
Preparing initial states

        Total bins:            135
        Initial replicas:      5 in 1 bins, total weight = 1
        Total target replicas: 675
       
1-prob: 0.0000e+00
Simulation prepared.
1 of 135 (0.740741%) active bins are populated
per-bin minimum non-zero probability:       1
per-bin maximum probability:                1
per-bin probability dynamic range (kT):     0
per-segment minimum non-zero probability:   0.2
per-segment maximum non-zero probability:   0.2
per-segment probability dynamic range (kT): 0
norm = 1, error in norm = 0 (0*epsilon)
WESTPA environment activating ...
WESTPA environment active! :)
Updating system with the options from the configuration file
Maximum wallclock time: 3 days, 0:00:00

Wed Jan 28 09:39:43 2026
Iteration 1 (200 requested)
Beginning iteration 1
5 segments remain in iteration 1 (5 total)
1 of 135 (0.740741%) active bins are populated
per-bin minimum non-zero probability:       1
per-bin maximum probability:                1
per-bin probability dynamic range (kT):     0
per-segment minimum non-zero probability:   0.2
per-segment maximum non-zero probability:   0.2
per-segment probability dynamic range (kT): 0
norm = 1, error in norm = 0 (0*epsilon)
Waiting for segments to complete...
-- ERROR    [westpa.core.propagators.executable] -- could not read pcoord for Segment 3 from '/tmp/tmpgu4ggtbt': ValueError('cannot reshape array of size 0 into shape (101,2)')
-- ERROR    [westpa.core.propagators.executable] -- could not read pcoord for Segment 0 from '/tmp/tmpmw1w647w': ValueError('cannot reshape array of size 0 into shape (101,2)')
-- ERROR    [westpa.core.propagators.executable] -- could not read pcoord for Segment 1 from '/tmp/tmpu37nc8dw': ValueError('cannot reshape array of size 0 into shape (101,2)')
-- ERROR    [westpa.core.propagators.executable] -- could not read pcoord for Segment 4 from '/tmp/tmpqg64f98w': ValueError('cannot reshape array of size 0 into shape (101,2)')
-- ERROR    [westpa.core.propagators.executable] -- could not read pcoord for Segment 2 from '/tmp/tmpgl7c2954': ValueError('cannot reshape array of size 0 into shape (101,2)')
-- ERROR    [westpa.core.sim_manager] -- propagation failed for 5 segment(s):
0  
1  
2  
3  
4
exception caught; shutting down
-- ERROR    [w_run] -- error message: propagation failed for 5 segments
-- ERROR    [w_run] -- Traceback (most recent call last):
  File "/home/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/cli/core/w_run.py", line 61, in run_simulation
    sim_manager.run()
  File "/home/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/core/sim_manager.py", line 769, in run
    self.check_propagation()
  File "/home/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/core/sim_manager.py", line 667, in check_propagation
    raise PropagationError('propagation failed for {:d} segments'.format(len(failed_segments)))
westpa.core.sim_manager.PropagationError: propagation failed for 5 segments

I hope this is not a repeat thread ( I didn't find anything that quite answered my question), please refer me to an existing thread if  there is one. Any  pointers would be appreciated, thank you!

[Leung, Jeremy]

Hi Shashank,

Welcome!

You are indeed implementing it incorrectly.  When passing to $WEST_XXXX_RETURN, you are saving it as auxdata. (This is also assuming you have correctly configured the dataset in west.cfg https://github.com/westpa/westpa/wiki/Configuration-File#data-manager).  It's good practice to keep a copy of it there, but more importantly, you need to send both columns to $WEST_PCOORD_RETURN to be used the pcoord. Tutorial 5.2 (The one by p53) should be a good example to follow.

```

paste <(cat ca-rmsd-p53.dat | tail -n +2 | awk {'print $2'}) <(cat dist-end-to-end.dat | tail -n +2 | awk {'print $2'})>$WEST_PCOORD_RETURN

```

I'm assuming your `get_pcoord.sh` is formatted a bit differently (and may be correct) so you're passing `w_init`. Please double check in your west.h5 (via command line here): `h5ls -d west.h5['ibstates/0/bstate_pcoord']` that the correct pcoord is passed to WESTPA.  (for other options, see https://github.com/westpa/westpa/wiki/Navigating-the-west.h5-File)

Best,

Jeremy L.

---
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]

On Jan 28, 2026, at 10:57 AM, Shashank Shastry <ss...@illinois.edu> wrote:

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