[gmx-users] PCA

francesco oteri francesco.oteri at gmail.com
Tue Nov 6 10:25:21 CET 2012

Hi Tuba,
I guess you have to create an index for each peptide and then
extracting covariance matrix on each peptide using the new indexes.


2012/11/6 Tuba Kilinc <tkilinc at gmail.com>

>  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 ?
> thanks
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Cordiali saluti, Dr.Oteri Francesco

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