Apparent convergence issues

[amin-sagar]

Hello.

I tried doing a protein-peptide FEP (#682 )
I initially tried with the standard 11 replicas/lambda states.

This seems to suggest not enough overlap between the replicas, so I increased the number to 15 and then 21 using

protocol_settings.simulation_settings.n_replicas = 21
protocol_settings.lambda_settings.lambda_windows = 21

Now, I get

The timeseries plot seems to show exchanges but the transition matrix is mostly empty.
It doesn't seem like the transitions are 0 for the initial replicas.
Why could this be happening?
I would be really grateful for any suggestions.
Best,
Amin.