I have calculated the transition matrix of a Markov state model with four metastable states. I would like to know the probability of transition between metastable states, for which I think I should obtain a 4x4 matrix.
I have tried to obtain said matrix with this code, but it turns out that in some entries of that matrix values greater than 1 appear, which seems strange to me:
nstates = 4transition_matrix_meta = np.zeros((nstates, nstates))for i in range(nstates):for j in range(nstates):
pi_i = msm.pi[msm.metastable_sets[i]].sum() T_i_to_j = msm.transition_matrix[msm.metastable_sets[i]][:, msm.metastable_sets[j]] P_i_to_j = pi_i * T_i_to_j.sum() transition_matrix_meta[i, j] = P_i_to_j
print(transition_matrix_meta)
Is my code correct?