MC.
_log_likelihood_z
(model, temp=None)¶This function estimate the likelihood of the current free energy or diffusion profile over the bins in a simulation box. It is used to calculated the diffusion in z-direction over z-coordinate. This likelihood is necessary to decide whether the MC step will be accepted.
with \(R\) as the rate matrix from _init_rate_matrix_pbc()
,
\(\Delta_{ij}t_{\alpha}\) as the current lag time and
\(N_{ij}(\Delta_{ij}t_{\alpha})\) as the transition matrix.
The transition matrix contains the numbers of all observed transition
\(j \rightarrow i\) at a given lag time in a simulated trajectory.
This matrix is sampled with the function poreana.sample.Sample.init_diffusion_mc()
from
a simulated trajectory at the beginning and depends on the lag time.
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