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2024-05-03
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2024-05-02
Editing revision 25 of Tools and methods for analysing MD simulations
Editing old revision 25. Saving this page will replace the latest revision with this text.
Please add other analyses, other methods/programs for performing the same task, etc. * [[Quick view of large trajectory (DCD) files]] * [[Preparing a protein-only DCD file (removing waters)]] * [[Removing global rotations-translations from a protein-only DCD file]] * [[Removing global rotations-translations using selected atoms for fitting]] * [[Calculation of rmsd from the starting structure]] * [[Calculation of the average structure and corresponding fluctuations]] * [[Calculation of rmsd from the average structure]] * [[Calculation of the evolution of the radius of gyration]] * [[Calculation of the average Cα-Cα distance map and the corresponding rmsd]] * [[Calculation of frame-to-frame rmsds]] * [[Variance-covariance and cross-correlation analysis]] * [[Variance-covariance analysis and comparison with experimental results]] * [[Principal component analysis]] * [[Calculation of eigenvalues and eigenvectors]] * [[More on eigenvectors and eigenvalues]] * [[Eigenvectors and eigenvalues, sufficient sampling issues]] * [[Comparison of sets of eigenvectors]] * [[φ,ψ time series]] * [[χ-value analysis (including χ1-χ2 plots and residence times)]] * [[Cluster analysis of trajectories]] * [[Secondary structure analysis of protein trajectories]] * [[Anisotropic fluctuations (and their visualisation)]] * [[Calculation of water and ion distributions]]
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