Dear Tsjerk, Thank you very much for the explanation.
So, in other words, as I have carried out PCA on the basis of CA atoms from the MD trajectory, so if I wish to project the crystal structure onto the EV, then I need to consider only the CA atoms of the crystal structure (which in that case won't be the exact crystal structure) as well. Right? Thanks a lot again. Regards, Anirban On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Anirban, > > The eigenvectors obtained from the simulation are a way of rewriting the > coordinates of your structures, not in terms of atoms-XYZ, but as > combinations of these. Because they are combinations of atom-positions, > they are defined for the selection of atoms used for the calculation. If > your crystal structure has the same atoms, which is true if you did not use > hydrogen atoms, or modeled parts for the covariance analysis, then you can > project that structure onto the eigenvectors determined, in exactly the way > you describe in your question. > > Hope it helps, > > Tsjerk > > > > On Thu, Jun 6, 2013 at 12:06 PM, Anirban <reach.anirban.gh...@gmail.com > >wrote: > > > Hi ALL, > > > > I have carried out a simulation of a protein and have carried out PCA on > > the entire trajectory. I have obtained a 2D projection plot of EV1 on > EV2. > > Now I want to locate the conformation of the crystal structure (with > which > > I started the MD) on this map. How to do this? Can I use "g_anaeig -v > > Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx > > -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure > position? > > Or do I need to calculate covariance matrix for the crystal str.(I need a > > set of them in that case) and then use g_anaeig? > > Thanks a lot in advance. > > > > Regards, > > > > Anirban > > -- > > 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. > -- > 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 > -- 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