MBG wiki: 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.

Username:

Replace this text with a file.