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
Resources
Undergraduate
Chemical Engineering Thermodynamics by J. M. Smith and others
Chemical Reaction Engineering by Octave Levenspiel
Numerical Methods in Engineering and Science by B. S. Grewal
An Introduction to Statistical Learning with Applications in Python or R by Gareth M. James and others
Postgraduate
An Introduction to Statistical Thermodynamics by Terrell L. Hill
Statistical Mechanics by Donald A. McQuarrie
Understanding Molecular Simulation from Algorithms to Applications by Berend Smit and Daan Frenkel
Intermolecular and surface forces by Jacob N. Israelachvili
Elements of Nonequilibrium Statistical Mechanics by V. Balakrishnan
Introduction to Statistical Machine Learning by Masashi Sugiyama
Writing
English Grammar & Composition by WREN & MARTIN
The Elements of Style by E. B. White and William Strunk Jr.
Links
Gromacs tutorials by Justin A. Lemkul --> Must for the beginners
WHAM code by Alan Grossfield --> He has implemented 2D WHAM and bootstraping analysis
OpenMM tutorials
OpenSMOG tutorial
Submit Python code to generate various CG models
Multi-eGO model development
Charmm-GUI lectures
Martini FF tutorials