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2024-03-19
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2024-03-18
Editing Tools and methods for analysing MD simulations
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]]
Summary:
This change is a minor edit.
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