MDProcessing is implemented in Python for the pre- and post-processing of molecular dynamics simulations and provides a variety of basic and advanced functionalities, with further developments planned.
Weighted Histogram Analysis Method (WHAM)
The current version supports reweighting in 1 collective variable and temperature space, offering flexibility in defining different biasing potentials. Some essential features will be added in future updates. Feel free to reach out if you need help, have suggestions, or want to report a bug.
Multidimensional Temperature-Accelerated String Method (TASM)
The method is used to identify multiple transition pathways connecting two known metastable states in an N-dimensional collective-variable space, to compute the corresponding minimum free-energy paths (MFEPs), to estimate the associated free-energy landscapes, and to calculate the effective transition rates using Kramers theory.
If the underlying function of a 2D landscape is unknown and only sparse data points are available, this code helps find the minimum-energy/free-energy path (MEP/MFEP) connecting two endpoints in the landscape. It is useful for analyzing free-energy surfaces, transition pathways, and other problems where one wants to connect metastable states through a smooth path.
This code applies the Multistate Bennett Acceptance Ratio (MBAR) in both the temperature and multidimensional collective variable (CV) spaces. I suggest using this over WHAM, especially if you are working with more than 1 CV.