[gmx-users] PCA

[Tsjerk Wassenaar]

Hi Tuba,

You can concatenate the trajectories with trjcat and perform PCA on
the resulting trajectory.

Cheers,

Tsjerk

On Thu, Oct 18, 2012 at 9:07 AM, Tuba Kilinc <tkilinc at gmail.com> wrote:
> 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
>  g_covar -s protein.pdb -f traj.xtc -v eigenvec.trr
>
> and i create projections on PCA vectors using g_anaeig.
>
> thanks
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada