Ah, so, right, you'll have to extract a trajectory for each peptide and concatenate those trajectories.
Sorry for misreading... Tsjerk On Thu, Oct 18, 2012 at 9:44 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > 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 <tkil...@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 >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
