MBG wiki | RecentChanges | Blog | 2021-09-24 | 2021-09-23

Tools and methods for analysing MD simulations

Difference (from prior major revision)

Added: 0a1,5

> 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]]

Added: 2a8,24

> * [[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]]


Please add other analyses, other methods/programs for performing the same task, etc.