Quick Reaction Coordinate using Python
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Updated
Jun 23, 2024 - Python
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reaction-coordinate
Here are 4 public repositories matching this topic...
Binless weighted histogram analysis method (WHAM) aka multi-state Bennet acceptance ratio (MBAR) with the ability to combine umbrella sampling simulations with different restraints and project onto reaction coordinates other than ones sampled at
statistics dynamics molecular pmf free-energies mbar reaction-coordinate weighted-histogram-analysis
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Jun 27, 2018 - Python
Simulation of block copolymer escape dynamics using a bead-spring model with Monte Carlo and forward-flux sampling. Includes free-energy profiling via umbrella sampling and escape rate estimation from micelle cores.
statistical-mechanics computational-physics monte-carlo-simulation stochastic-processes umbrella-sampling molecular-modeling self-consistent-field-theory reaction-coordinate polymer-dynamics block-copolymer forward-flux-sampling free-energy-profile escape-rate
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May 25, 2025 - Python
A clean Jupyter notebook demonstrating how to construct and visualise reaction free-energy profiles (ΔG) using Python, NumPy, and Matplotlib. Includes examples of two-path, branched, and three-way cheletropic/Diels–Alder mechanistic pathways, with Hartree-to-kJ/mol conversion, safety checks, smoothing functions, and publication-quality figures.
python chemistry data-visualization scientific-visualization computational-chemistry matplotlib physical-chemistry reaction-coordinate reaction-profiles energy-diagrams mechanistic-chemistry
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Nov 17, 2025 - Jupyter Notebook
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