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.
This includes a detailed tutorial on computing transition paths for protein conformational changes. The methodology is illustrated using alanine dipeptide and can be readily extended to more complex protein systems.
Under progress ...
Tutorial and Teaching
I am working on designing the following tutorials and teaching materials:
A step-by-step guide to membrane protein simulations using both all-atom and coarse-grained force fields
Python for beginners, including the underlying mathematical foundations
Classical optimization methods and machine learning techniques
Probability theory for deep learning
Classical and statistical thermodynamics