Gmx covar analysis- please help!

GROMACS version:5.0.7
GROMACS modification: Yes/No
Hi there,

This is my first time doing a PCA/Covariance analysis of a 20ns Protein-Ligand simulation using gmx covar and gmx anaeig commands from Gromacs. From all the selections that the commands gave, I have chosen backbone. The resulting plots are attached. Plot 1 is eigenvectors vrs eigenvalues and plot2 is the 2d scatter plot. Yellow is my reference and blue and green are my hit molecules.


I read a few research articles and I understood about the scatter plot that my hit molecules are taking up lesser conformational space than reference; which is good. But what does the first plot mean? Like i understand that first few eigen vectors contribute to the change in protein dynamics upon ligand binding, but won’t that be a stabilization effect? i would really appreciate if someone could help me analyse these plots in layman terms.


A good step to start is trying to translate back what you see into a structural change. Try to anlayse what movement the different axis describe - you can identify the frames corresponding to the leftmost and rightmost points in your landscape and have a look what structures they represent.

It might be helpful to have a look at some articles that use PCA to understand how you can interpret the results from this analysis, you can e.g. have a look at this one:

Thank you @cblau for you reply. i did try to align and superimpose my representative structures but there wasn’t any structural difference per se.