[gmx-users] PCA

Tuba Kilinc tkilinc at gmail.com
Tue Nov 6 08:58:51 CET 2012

 hi all,

i would like to apply PCA (principal component analysis) for my peptides
that i simulated. i do know PCA for one trajectory but what if i have more
than one peptide ? how can i apply pca for example 10 peptides in a box ?
typically, i start with a PCA on the simulation with

g_covar -s protein.pdb -f traj.xtc -v eigenvec.trr

and i create projections on PCA vectors using g_anaeig
i have to extract a trajectory for each peptide and concatenate those
trajectories and i need to  make an index group for each peptide in each
system that i  include but i couldnt figure out  extract a trajectory for
each group for each system? Could you help me please ?

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