Essential Dynamics Analysis

In this part, we will perform essential dynamics analysis calculations for a p38 MAP kinase trajectory and compare results with normal modes from ANM calculations. You will need following files:

This files contain frame from a 40 ns long simulation of p38. Detailed analysis of this trajectory can be found in [AB11].

Load the contents of this file into VMD as follows:

$ vmd p38.pdb p38_100frames.dcd

Click on ProDy Interface for performing ANM and EDA jobs.

[AB11]Bakan A, Bahar I. Computational generation of inhibitor-bound conformers of p38 MAP kinase and comparison with experiments. Pacific Symposium on Biocomputing 2011 16 181-192.

EDA Calculation

Select PCA Calculation in the ProDy Job Settings panel. Set First frame 1 to exclude the X-ray coordinates from the calculation. You may also check aligned to make ProDy skip alignment step in PCA/EDA calculations when you already have done the alignment in VMD. In this case, the frames are already aligned. Click Submit Job and results will be loaded automatically when prody pca command finishes the calculations.

ANM Calculation

We will perform ANM calculations for all Cα atoms and keep the rest of the parameters unchanged. To properly align the structures used for EDA and ANM, set First frame to 100 for the ANM calculation. Click Submit Job and results obtained from prody anm command will load automatically.


EDA 1 (orange) vs. ANM mode 1 (lime green)


For each dataset you load into or generate via NMWiz, a GUI will pop up with independent controls for normal mode display, animation, and plotting. Select PC 1 and ANM mode 1 and try to get the view in the image in VMD display.


NMWiz writes a DCD or PDB file for PCA/EDA calculations. For large systems and long trajectories you may try one or more of the following for speedier calculations:

  • select a subset of atoms, e.g. Cα atoms
  • select a subset of frames, e.g. set Skip frame a value greater than 0
  • use DCD file for faster IO operations and less disk usage
  • alternatively, if you have trajectories in DCD format, use prody pca directly to obtain results in NMD Format