I performed MD of a protein-ligand complex in Gromacs.

I generated the RMSD curve using this command.

· gmx rms -f traj.xtc -s md.tpr -n index.ndx -tu ns -o rmsd.xvg

Least square fit: Backbone | RMSD calculation: ligand

Later I performed PCA for Free Energy Landscape analysis using following commands

• · gmx covar -f traj.xtc -s md.tpr –o eigenvalues.xvg -v eigenvectors.trr -xpma covapic.xpm -n index.ndx

• · gmx anaeig -f traj.xtc -s md.tpr -v eigenvectors.trr -last 1 -proj pc1.xvg -n index.ndx

• · gmx anaeig -f traj.xtc -s md.tpr -v eigenvectors.trr -first 2 last 2 -proj pc2.xvg -n index.ndx

• · paste pc1.xvg pc2.xvg | awk ‘{print $1, $2, $4}’ > pc1pc2.xvg

• · gmx sham -f pc1pc2.xvg -ls FES.xpm

Now, instead of PC1 and PC2, I want to generate FEL using RMSD and Rg.

What changes should I make in my commands?