Downloads

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

[movie]

BayesWHAM

[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.

[https://bitbucket.org/andrewlferguson/bayeswham_matlab]
[https://bitbucket.org/andrewlferguson/bayeswham_python]

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] [http://dx.doi.org/10.1002/jcc.24800]

[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.

[https://bitbucket.org/andrewlferguson/bayeswham_matlab_v2]

Diffusion Maps

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

[https://github.com/awlong/DiffusionMap]

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

[https://bitbucket.org/andrewlferguson/viralfitness_matlab]

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

[http://andrewlferguson.pythonanywhere.com/]

Ferguson Lab