├── README.md ├── examples └── liquid-argon │ ├── README.md │ ├── analyze-1.py │ ├── analyze-2.py │ ├── analyze-3.py │ ├── analyze-4.py │ ├── cleanup.sh │ ├── data.nc │ ├── environment.yml │ ├── equilibration.py │ ├── figures │ ├── argon-bias-variance.pdf │ ├── argon-density.pdf │ ├── argon-potential-bias-variance.pdf │ ├── argon-potential-reverse-cumulative-average.pdf │ ├── argon-potential-rmse.pdf │ ├── argon-potential.pdf │ ├── argon-reverse-cumulative-average.pdf │ ├── argon-rmse.pdf │ ├── toc-graphic.pdf │ └── toc-graphic.tiff │ ├── generate-toc-graphic.py │ ├── reproduce.sh │ ├── simulate.py │ ├── submit-torque.sh │ └── utils.py ├── manuscripts ├── Author_Corrections_template.rtf ├── README.md ├── automatic-equilibration-detection-doublespaced.pdf ├── automatic-equilibration-detection.bib ├── automatic-equilibration-detection.pdf ├── automatic-equilibration-detection.tex ├── automatic-equilibration-detectionNotes.bib ├── cover-letter.md ├── figures │ ├── argon-bias-variance.jpg │ ├── argon-bias-variance.pdf │ ├── argon-density.pdf │ ├── argon-potential-bias-variance.pdf │ ├── argon-potential-reverse-cumulative-average.pdf │ ├── argon-potential-rmse.pdf │ ├── argon-potential.pdf │ ├── argon-reverse-cumulative-average.pdf │ ├── argon-rmse.pdf │ ├── toc-graphic.pdf │ └── toc-graphic.tiff ├── plos2009.bst ├── prsty.bst ├── pymbar_example.py └── toc-graphic.tiff └── references ├── chodera-wham.pdf ├── geyer-burn-in-unnecessary.pdf ├── geyer-mcmc-handbook-chapter-1.pdf ├── geyer-practical-mcmc.pdf ├── packmol.pdf ├── skeel-equilibration.pdf ├── thompson-comparison-of-autocorrelation-time-estimators.pdf └── yang-karplus-rca.pdf /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/choderalab/automatic-equilibration-detection/HEAD/README.md -------------------------------------------------------------------------------- /examples/liquid-argon/README.md: 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