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
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