GROMACS modification: Yes/No
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.