#
# Example of "matrix" functionality in ptraj 
#   (Please note - the trajectory was aligned against
#    a reference structure before; otherwise use the
#    "rms" command to obtain meaningful results)
#
trajin 1rrb_vac.mdcrd

#
# Generate distance matrix of all CA atoms
#
matrix dist @CA out 1rrb_vac_distmat.dat

#
# Generate mass-weighted covariance matrix of all atoms,
#   which is stored internally, and subsequently 
#   analyzed (i.e. in total a quasiharmonic analysis is 
#   performed)
#
matrix mwcovar name 1rrb_vac_mwcovarmat out 1rrb_vac_mwcovarmat.dat
analyze matrix 1rrb_vac_mwcovarmat out 1rrb_vac_mwcovarmat_evecs.dat vecs 5 thermo

#
# Generate distance-covariance matrix of CA atoms,
#   which is stored internally, and subsequently analyzed
#   (i.e. a PCA in distance space is performed).
#   Eigenvectors are then reduced.
#
matrix distcovar :1-76@CA name 1rrb_vac_distcovarmat out 1rrb_vac_distcovarmat.dat
analyze matrix 1rrb_vac_distcovarmat out 1rrb_vac_distcovarmat_evecs.dat vecs 5 reduce