Dear All, I would like to get information on how g_covar calculates the average structure file (average.pdb)
My aim was actually to get a covariance matrix (<deltaR*deltaR>) so I started off by writing my own code, I use MDAnalysis package, so I give psf and traj files as an input and I generate the coordinates for each frame, and if I have 3 frames, I take the average of each coordinate element for 3 frames. So for the 1st CA atom, I have x, y, z values for 3 frames. So I add x1, x2, x3 values and divide by the number of frames. So this gives me the average x coordinate of the 1st CA atom. I do the same for y and z and then for all CA atoms. So if x1, x2, x3 for CA1 is 49.5 49.0 and 49.4 for 3 frames, the average x i get is 49.3. This is what I call an average structure. After doing this, I wanted to compare this with what g_covar gives me (average.pdb) but found out that the result that I get from my own calculations and the result I get from g_covar are very very different. The g_covar command that I use is the following: g_covar -f traj.xtc -s topol.tpr -ascii covar.dat -xpm covar.xpm -noref Here I use -noref because I already use trjconv on my initial trajectory to generate a new trajectory so I do -pbc mol and center and -fit rot+trans to remove translation, rotation and to fit the structure. So I thought I could use -nofit in g_covar to not to fit to the reference structure again. So, coming back to my question, why would g_covar give me a very different result than what I find with my simple code? What does g_covar do to calculate this average structure? I thought maybe it does some fitting or additional stuff to what I'm doing in my code or changes the units, that in the end it doesn't give me the same coordinates for the average.pdb. ----- Deniz Aydin, BSc. Graduate Student Chemical & Biological Engineering Graduate School of Sciences and Engineering Koç University, Istanbul, Turkey -- View this message in context: http://gromacs.5086.x6.nabble.com/g-covar-average-pdb-calculation-tp5011339.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
