[gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

[Qasim Pars]

Dear gmx users,

I have simulated three systems. The projection of each individual
trajectory on the first two eigenvectors obtained from the concatenated
trajectory is strange because each projection should start at (0,0) points
or near (0,0). Please have a look at the plot
https://www.dropbox.com/s/3jrlkdwbv4csccq/pca.png?dl=0

Why the projections do not start at (0,0) points or near (0,0)? Can anyone
of you tell me where I might have made a mistake?

In order to remove jumps across the box of each trajectory I used the gmx
trjconv -pbc nojump. The other commands are below:

trjcat -f wt.xtc one-ligand.xtc two-ligands.xtc -o merged.xtc -cat

gmx covar -f merged.xtc -s wt.pdb

gmx anaeig -f wt.xtc -s wt.pdb -v eigenvec.trr -2d wt.xvg -first 1 -last 2
gmx anaeig -f one-ligand.xtc -s wt.pdb -v eigenvec.trr -2d one-ligand.xvg
-first 1 -last 2
gmx anaeig -f two-ligands.xtc -s wt.pdb -v eigenvec.trr -2d two-ligands.xvg
-first 1 -last 2

Cheers,

-- 
Qasim Pars