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Bayesian Reweighting with Gibbs Sampler (Bayesian approach to WHAM/MBAR/etc)
Generalized WHAM or non-parametric reweighting (with a Bayesian bootstrapping algorithm)
Contour: A program for plotting 2D free energy maps and minimum free energy pathways.
LFEP: A program for finding lowest free energy pathway from 2D free energy maps.
NMFEP: A non-parametric minimum free energy path finding algorithm for high-dimensional spaces.
Relative reaction rate estimator (with examples/tutorial)
Work calculation script for NAMD colvar module (Note: Reporting total work and biasing potential is enabled in NAMD 2.10xx; there is no need for this script now unless you want to decompose the work and biasing potential!)
Work calculation script for NAMD with examples
Exploring Complex Conformational Transition Pathways: NAMD scripts, tutorial, and examples for bias-exchange umbrella sampling (BEUS) and string method with swarms of trajectories (SMwST).
Please contact me if you are interested in using my code for post-hoc string method (PHSM).
Algorithms for AMBER (with examples/tutorial)
Molecular Dynamics Tutorials (including VMD, CHARMM-GUI, and NAMD)
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