Hi everyone,

After completing my MD simulation, I performed PCA using the following steps:

I first centered the protein-ligand complex using:

gmx trjconv -s MD.tpr -f MD.xtc -o MD_center.xtc -center -pbc mol -ur compact

Then I ran covariance analysis:

gmx covar -s MD.tpr -f MD_center.xtc -o eigenval.xvg -v eigenvec.trr -av average.pdb

After that, I projected the trajectory onto the first 5 principal components:

gmx anaeig -v eigenvec.trr -s MD.tpr -f MD_center.xtc -first 1 -last 5 -proj proj.xvg

This generated a .xvg file that contains numerical data. I have attached this file here for reference.

Could someone please confirm if I’ve followed the correct workflow? Also, I’d appreciate guidance on how to use this .xvg file to plot PC1 vs PC2, either using Python, R, or any GUI-based tool.

I’ve attached the .xvg file as well.

Thanks in advance!