Hi Chris, Carla, Sorry I didn't reply before. To understand the projections, first consider the following. Take a single atom with three coordinates (x,y,z). These coordinates are the projections onto a set of (three, Cartesian) axes. If you consider, e.g., the projection of the coordinates onto the x-axis, you're left with a single number in distance measure (nm in gromacs). Now let's say your coordinates are (1,1,1). If you then take the axis (x+y+z), rather than one of the original ones, and project your coordinates onto it, you get a projection of sqrt(3) nm. To describe all of Cartesian space, you need two more axes, orthogonal to x+y+z, but for this particular point the projections will both be zero. Now for a complete configuration, it's a bit more complicated. You best think of it as a point in 3N-dimensional space, having specific projections or scores on 3N mutually orthogonal axes. These projections still have the same units (nm). The aim of PCA is to find new axes in this space that better describe a distribution of these points, i.e. a set of configurations. Each configuration has one projection on each axis. If you only select one eigenvector, the projection will give a single number. Filtering is the next step. If you have a projection of a configuration onto a selected number of components, you can consider that as having the projections on all other axes set to zero. In other words, the variance or noise associated with these other axes is removed. If you project these projections back to the original space, then you've effectively filtered out the variance/noise.
I hope that clarifies a bit. > ### > > Tsjerk: First, great tutorial, I hadn't seen this before. Second, you might > avoid this type of confusion by mentioning during the command: Thnx :) > g_anaeig -s ../topol.tpr -f ../traj.xtc -v eigenvectors.trr -eig > eigenvalues.xvg -proj proj-ev1.xvg -extr ev1.pdb -rmsf rmsf-ev1.xvg -first 1 > -last 1 > > that you care actually doing a few things at once... or perhaps actually > break the command apart into separate g_anaeig -proj and g_anaeig -extr > calls. > > ### Agreed. It's probably best to have the different operations split. > All: might it be a good idea to get the html addresses of nice tutorials > into the output messages of the analysis tools? That would only make sense if the tutorials are adopted and put on the gromacs site. Otherwise the tutorials/sites are probably too volatile. Adoption raises questions regarding responsibility and maintenance though. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
