Hi Deniz, The option -ref/-noref is not what you think it is. You want to use -nofit.
Cheers, Tsjerk On Fri, Sep 20, 2013 at 2:26 PM, Deniz Aydin <denizay...@ku.edu.tr> wrote: > 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 > -- 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
