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Biomolecular Simulations Group

Codes and Scripts:

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

Please contact me if you are interested in my NAMD scripts for bias-exchange umbrella sampling and string method with swarms of trajectories as well as my code for post-hoc string method.

New Algorithms for AMBER (with examples/tutorial)

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