Thermo package (pyemma.thermo)¶
The thermo package provides functions to analyze data originating from potentially biased multi-ensemble MD-Simulations.
User-Functions¶
For most users, the following high-level functions are sufficient to estimate models from data.
estimate_umbrella_sampling(us_trajs, ...[, ...]) |
Wraps umbrella sampling data or a mix of umbrella sampling and and direct molecular dynamics. |
estimate_multi_temperature(energy_trajs, ...) |
Wraps multi-temperature data. |
dtram(ttrajs, dtrajs, bias, lag[, maxiter, ...]) |
Discrete transition-based reweighting analysis method |
wham(ttrajs, dtrajs, bias[, maxiter, ...]) |
Weighted histogram analysis method |
Thermo classes¶
Estimators to generate models from data. If you are not an expert user, use the API functions above.
StationaryModel([pi, f, normalize_energy, label]) |
StationaryModel combines a stationary vector with discrete-state free energies. |
MEMM(models, f_therm[, pi, f, label]) |
Coupled set of Models at multiple thermodynamic states |
WHAM(bias_energies_full[, stride, maxiter, ...]) |
Weighted Histogram Analysis Method |
DTRAM(bias_energies_full, lag[, count_mode, ...]) |
Discrete Transition(-based) Reweighting Analysis Method |