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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

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).

New Algorithms for AMBER (with examples/tutorial)

Trialanine String Method Pathway: (Result of 100 iterations of SMwST - Contains configuration files, SM code, and xsc/vel/coor files)

CoV2 String Method Pathway: (First 1000 replicas - Result of 200 iterations)

Copyright © 2015, Biomolecular Simulations Group, Department of Chemistry and Biochemistry, University of Arkansas.
These materials are not endorsed, approved, sponsored, or provided by or on behalf of the University of Arkansas, Fayetteville.
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