What is the meaning of "Normal mode analysis"?

[Cheng]

Dear All,

Sorry, I have been searching information on the NMA but could not find good answer to explain the concept of NMA. I was trying to capture the NMA idea without looking into the equations. Is this possible? I also find it seems to be similar to PCA.

Let's say a protein with 100 residues. I have an ensemble of trajectories (e.g. PDB coordinates) from an MD simulation. After running the PCA for the C-alpha atom coordinates (i.e. 100x3=300), I get 300 principal components, with the first component, i.e. PC1, capturing the largest variations across the 300 dimensions.

So if I run NMA, what can I get?

In the paper Normal mode analysis for proteins, it says: NMA of proteins is based on the hypothesis that the vibrational normal modes exhibiting the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant. So does it mean, the motion with lower frequencies would have larger magnitude? I think this is not always true.

[Barry Grant]

Of topic: not about bio3d