library(bio3d)
## reads a PDB file as reference. must have the same number of atoms as your trajectory file
pdb <- read.pdb("Pdb_file_with_the_same_number_of_atoms.pdb")

## reads your trajectory
trj <- read.dcd("my_nice_dcd_traj_file")

## finds the CA atoms
ca.inds <- atom.select(pdb, "calpha")

## performs the PCA
pc.traj <- pca.xyz(trj[, ca.inds$xyz])

## plots it
plot(pc.traj)

## make a trajectory for visualization in VMD
a <- mktrj.pca(pc.traj, pc=1, file="pc1.pdb")