[gmx-users] Problems with Jacobi diagonalization

[Dayle Smith]

 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 <tsjerkw at gmail.com> 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 <daylemariesmith at gmail.com>:
> > 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 <Mark.Abraham at anu.edu.au>
> > 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
> >> _______________________________________________
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>
>
> --
> 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
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