Hi Bharat, On Tue, Feb 1, 2011 at 8:33 AM, bharat gupta <bharat.85.m...@gmail.com> wrote: > Hi, > After searching though gmxuserlist I found the relevant thread for ED... I > followed the following steps :-
What thread are you referring to? > 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha > atoms only) > 2) g_anaeig - to generate eigen vectors g_covar calculates the eigenvectors. It's what you end up with through diagonalization. > 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at > this step that - g_rmsf is not for calculating RMSD, and hasn't got much to do with eigenvector analysis. That's what g_anaeig is for (like with the option -rmsf). Using g_anaeig will avoid the error you observe. As a side note, 3 ns is rather short for this sort of thing. You have to check the cosine content of the first principal components to see if you've reached equilibrium already. 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
