[gmx-users] PCA

vijaya subramanian vijaya65 at hotmail.com
Tue Nov 6 18:01:08 CET 2012

use make_ndx to create a new group, then use the -n index.ndx option with g_covar

> Date: Tue, 6 Nov 2012 09:58:51 +0200
> From: tkilinc at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] PCA
>  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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