IndexError: index 188 is out of bounds for axis 0 with size 184

[vas2201]

HI ,

I am getting following error, while doing msm analysis, Could you please suggest me how to fix this error ?

Regards
Vas

---

IndexError Traceback (most recent call last)
Cell In[39], line 4
1 fig, axes = plt.subplots(1, 2, figsize=(10, 6), sharex=True, sharey=True)
2 pyemma.plots.plot_contour(
3 *tica_concatenated[:, :2].T,
----> 4 msm.pi[dtrajs_concatenated],
5 ax=axes[0],
6 mask=True,
7 cbar_label='stationary distribution')
8 pyemma.plots.plot_free_energy(
9 *tica_concatenated[:, :2].T,
10 weights=np.concatenate(msm.trajectory_weights()),
11 ax=axes[1],
12 legacy=False, kT=0.6, cbar_label='Free Energy (kcal/mol)')
13 for ax in axes.flat:

IndexError: index 188 is out of bounds for axis 0 with size 184

[vas2201]

use msm.pi[np.concatenate(msm.dtrajs_active)] instead.

[AChatzigoulas]

Is there a way to keep all microstates? I tried using mincount_connectivity=0 in bayesian_markov_model() but it didn't change anything.

[clonker]

For it to be a valid msm with associated stationary distribution over all states you need regularization or ideally more statistics. It'll currently subselect the largest set of micro states which are still connected. Mincount connectivity in that sense is a misleading name, it means that it there are strictly more than 0 counts it's deemed connected