LAMMPS Tutorial
MD Primer
Primer on the molecular dynamics method
[movie]
[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]
[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]
[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]
[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/]
[http://andrewlferguson.pythonanywhere.com/]
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
[https://github.com/cwangjiang/TakensFES]
J. Wang and A.L. Ferguson* "Nonlinear reconstruction of single-molecule free energy surfaces from univariate time series" Phys. Rev. E 93 032412 (2016) [http://link.aps.org/doi/10.1103/PhysRevE.93.032412]
[https://github.com/cwangjiang/TakensFES]
J. Wang and A.L. Ferguson* "Nonlinear reconstruction of single-molecule free energy surfaces from univariate time series" Phys. Rev. E 93 032412 (2016) [http://link.aps.org/doi/10.1103/PhysRevE.93.032412]