[gmx-users] PCA problems

[ingram]

Dear GROMACS community

I am trying to complete a PCA analysis of my peptide adsorbed to a 
surface. However when I use :

gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc

and select the protein for both the least squares fit and covariance 
calculation, followed by


gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro 
-first 1 -last 1 -skip 100

and I select the peptide for the least squares and covariance 
calculation

My peptide is now broken up into pieces. Is this right?



Best
Teresa