Thanks a lot Tsjerk :) -Anirban
On Thu, Jun 6, 2013 at 4:42 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Anirban, > > Indeed. > > :) > > Tsjerk > > > On Thu, Jun 6, 2013 at 1:11 PM, Anirban <reach.anirban.gh...@gmail.com > >wrote: > > > 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 > > > > > > -- > 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