├── .github └── workflows │ └── build-pdf.yml ├── .gitignore ├── LICENSE ├── README.md ├── figure ├── forcefield │ └── fig_biomol_model.pdf ├── sample │ └── sample_figure.pdf └── templete │ └── sample_figure.pdf └── src ├── .gitignore ├── .latexmkrc ├── README.md ├── analytical-mechanics ├── .latexmkrc ├── analytical-mechanics.bib └── analytical-mechanics.tex ├── auto-correlation-function ├── .latexmkrc └── auto-correlation-function.tex ├── constrain-dynamics ├── .latexmkrc ├── constrain-dynamics.bib └── constrain-dynamics.tex ├── dssp ├── .latexmkrc ├── dssp.bib └── dssp.tex ├── electrostatic-in-solution ├── .latexmkrc └── electrostatic-in-solution.tex ├── ewald ├── .latexmkrc ├── ewald.bib └── ewald.tex ├── extended-phase-space-method ├── .latexmkrc ├── extended-phase-space-method.bib └── extended-phase-space-method.tex ├── force-field ├── .latexmkrc ├── force-field.bib └── force-field.tex ├── generalized-ensemble ├── .latexmkrc ├── generalized-ensemble.bib └── generalized-ensemble.tex ├── include ├── begin.tex ├── end.tex ├── macro.tex ├── page-rayout.tex ├── preample-jsarticle.tex ├── preample-jsbook.tex └── usepackage.tex ├── integrator ├── .latexmkrc ├── integrator.bib └── integrator.tex ├── interpolation-methods ├── .latexmkrc └── interpolation-methods.tex ├── main.tex ├── markov-chain-monte-carlo ├── .latexmkrc └── markov-chain-monte-carlo.tex ├── modeling-molecules ├── .latexmkrc ├── modeling-molecules.bib └── modeling-molecules.tex ├── pca ├── .latexmkrc ├── pca.bib └── pca.tex ├── radius-of-gyration ├── .latexmkrc └── radius-of-gyration.tex ├── reweighting-technique ├── .latexmkrc ├── reweighting-technique.bib └── reweighting-technique.tex ├── rigid-body-MD ├── .latexmkrc ├── rigid-body-MD.bib └── rigid-body-MD.tex ├── rmsd ├── .latexmkrc ├── rmsd.bib └── rmsd.tex ├── simulation-basic ├── .latexmkrc ├── simulation-basic.bib └── simulation-basic.tex ├── solvent-accessible-surface-area ├── .latexmkrc ├── solvent-accessible-surface-area.bib └── solvent-accessible-surface-area.tex ├── statistical-mechanics ├── .latexmkrc ├── statistical-mechanics.bib └── statistical-mechanics.tex ├── symplectic ├── .latexmkrc └── symplectic.tex ├── template ├── .latexmkrc └── template.tex ├── thermodynamics-quantities ├── .latexmkrc ├── thermodynamics-quantities.bib └── thermodynamics-quantities.tex └── util-scripts ├── copy-pdffiles-githubio.sh ├── format-punctuation-all.sh ├── format-punctuation.sh ├── latexmk-alldocs.sh └── make-directory.sh /.github/workflows/build-pdf.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MasatakaYm/Molecular-Simulation/HEAD/.github/workflows/build-pdf.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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