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