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LAMMPS Tutorial
Molecular Dynamics with LAMMPS
Elements of Integrated Computational Materials Engineering Workshop, UIUC, 23-25 July 2014

workshop] [YouTube] [slides] [scripts]
MD Primer
Primer on the molecular dynamics method

[v1] Open source MATLAB and Python 2.7 implementations of a Bayesian implementation of the weighted histogram analysis method (WHAM) to estimate free energy surfaces (FES) from biased sampling data.


A.L. Ferguson* "BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method" J. Comput. Chem. 38 18 1583-1605 (2017) [pdf] []

[v2] Open source MATLAB generalization of BayesWHAM permitting incorporation of data at different T and P state points and extrapolative / interpolative estimation of unbiased FES at other T and P state points.

Diffusion Maps
Memory efficient C++ implementation of sparse diffusion maps using Armadillo libraries

Potts Spin Glass Viral Fitness Landscapes
MATLAB code to translate viral protein multiple sequence alignment into an empirical Potts spin glass model of viral fitness landscape

Support Vector Machine Antimicrobial Peptide (SVMAMP) Predictor
Python web tool for structure-free prediction of antimicrobial peptides based on a support vector machine (SVM) classifier

Takens' Attractor Reconstruction
Matlab codes to conduct Takens' delay embeddings, nonlinear dimensionality reduction, and diffeomorphism validation to reconstruct topologically equivalent attractors of dynamical systems from (univariate) time series measurements


J. Wang and A.L. Ferguson* "Nonlinear reconstruction of single-molecule free energy surfaces from univariate time series" Phys. Rev. E 93 032412 (2016) []