Hi there Tsjerk- There are a lot of helpful people on this list! I transferred my gromacs files to a different TeraGrid computer that runs gromacs-4.0.2, and now g_covar and the other diagonalizing routines work! I don't know what was wrong with gromacs-3.3.3 on that first computer, since I tried everyone's suggestions, and I sent a note to the system administrator. Thank you so much, Dayle
PS: Thanks A LOT for mentioning the pitfalls of using -ref with g_covar!!! That was a close one. On Thu, Apr 2, 2009 at 12:25 AM, Tsjerk Wassenaar <[email protected]> wrote: > Hi Dayle, > > Quite a number of posts here :) > > Okay, so there may indeed (still) be a mismatch. Maybe good noting > that g_covar will also accept a .pdb file as reference. One way to be > sure that things go right is to convert the .tpr to .pdb using the > index with the group 'TDR': > > editconf -f topol.tpr -o TDR.pdb -n index.ndx > > Then use that file to convert the trajectory to .pdb: > > trjconv -s TDR.pdb -f traj.xtc -o traj.pdb > > You should be fine taking the system as the atoms should match now. To > check if they do, visualize both topol.pdb and traj.pdb. You'll notice > a mismatch by garbled atom types/names. You have to explicitly check > for that. Such mismatches are a bit hard to spot, as the .xtc file > does not contain atom metadata. > > Aside of that there is another possible cause for this error to occur, > and that is when the system is split over the periodic boundaries. > That will also break the routine, but will also immediately show up > when visualizing the system as mentioned above. > > Then, by means of 'by the way', are you sure you want to use the -ref > flag with g_covar? This means that the deviations are taken with > respect to the reference coordinates rather than with respect to the > average coordinates. This comes down to calculating a non-central > second moment. To illustrate that, imagine tossing a dice to > investigate the distribution of numbers. Fine, you come to an average > and get the standard deviation the usual way. But what you do here is > calculating the deviation from, say 5, rather than the average of 3.5, > or worse even, from 8. Nice exercise to calculate the second moment > you get in that case and to try and think of what it means. I don't > say it has no meaning; in some cases it makes sense, but you'll have > to have good reasons for doing it and justify the approach when it > comes to publication. More so, it usually requires more thinking of > what such results signify. > > Cheers, > > Tsjerk > > > 2009/4/2 Dayle Smith <[email protected]>: > > Thanks, Mark- > > I re-ran a short MD simulation with TDR as the only xtc group, and used > > tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar > > with an index.ndx that contains only TPR (just to be safe!), > > > > g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx > > > > and I still get the Jacobi error: > > > > Choose a group for the least squares fit > > Group 0 ( TDR) has 29 elements > > There is one group in the index > > > > Choose a group for the covariance analysis > > Group 0 ( TDR) has 29 elements > > There is one group in the index > > Calculating the average structure ... > > Reading frame 0 time 0.000 > > ------------------------------------------------------- > > Program g_covar, VERSION 3.3.3 > > Source code file: nrjac.c, line: 129 > > > > Fatal error: > > Error: Too many iterations in routine JACOBI > > > > ~Dayle > > > > > > On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham <[email protected]> > > wrote: > >> > >> Justin A. Lemkul wrote: > >>> > >>> > >>> Dayle Smith wrote: > >>>> > >>>> Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 > atoms > >>>> in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is > >>> > >>> Indeed, that's the problem, then! > >>> > >>>> the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and > >>>> now gmxcheck shows that the number of atoms in topol.tpr is 12284, but > I > >>>> still can't get g_covar to work. Maybe these are unrelated problems, > I'm not > >>>> sure. > >>> > >>> You haven't really changed anything. The xtc-grps parameter defines > what > >>> was saved in the simulation. Setting it after the fact does not affect > the > >>> already-produced .xtc file. What you need is a .tpr file that contains > only > >>> TDR, so you would have to make modifications to your .top in order to > >>> generate this TDR-only .tpr file. > >> > >> Or use tpbconv - this is the "other" application for that utility. > >> > >> Mark > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> http://www.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 > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 >
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