Hi Thomas, > Thanks for all the clarifications about PCA you make on the mailing list!
Thank you for the appreciation :) > I have a question about the commandlines you wrote. Why do you use the .tpr > file with the "-s" flag? Is it because you want to compare the > mass-wheighted covariance matrices? I use to calculate the covariance > matrices by giving to g_covar a .pdb file with the "-s" flag and then > calculate the RMSIP without giving any structure file. I guess no masses are > used in that covariance analysis, right? Do you recommend using atom masses > for PCA in general? Well, I admit that in most cases I don't use mass-weighting myself. Unless you include hydrogens, it also doesn't matter much, as the masses are not very different. Only if you want to calculate frequencies, e.g. to connect to NMA and/or IR spectroscopy you would really need masses. If you use a .pdb or .gro file, you don't get mass-weighting. And you're right that for calculating the RMSIP, and the subspace overlap, and the martix of inner products, you don't need a structure filel, but only the eigenvectors, and possibly the eigenvalues. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
