Thermodynamic analysis tools for coarse grained modeling¶
The ‘foldamers’ package contains wide-ranging tools to analyze simulation data in order to estimate the thermodynamic properties of a system. In particular, the package leverages tools from pymbar to enable analysis of and estimate expectation values for sampled and unsampled thermodynamic states.
Using MBAR to compute expectation values for structural & thermodynamic properties¶
Shown below is the main ‘foldamers’ function used to re-weight simulation results with ‘pymbar’.
Evaluating thermodynamic properties with ‘pymbar’¶
Shown below ‘pymbar’-based tools/functions to evaluate thermodynamic properties within the ‘foldamers’ package.
Tools to evaluate thermodynamic properties with ‘pymbar’¶
Shown below are other ‘pymbar’-based tools/functions that aid evaluation of thermodynamic properties within the ‘foldamers’ package.
Calculating the heat capacity with pymbar¶
Shown below is the primary function used to evaluate the heat capacity with pymbar:
Shown below are functions/tools that can be used in order to calculate the heat capacity with pymbar.