Hi there Tsjerk-<br>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. <br>
Thank you so much,<br>Dayle<br><br>PS: Thanks A LOT for mentioning the pitfalls of using -ref with g_covar!!! That was a close one.<br><br><br><div class="gmail_quote">On Thu, Apr 2, 2009 at 12:25 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Dayle,<br>
<br>
Quite a number of posts here :)<br>
<br>
Okay, so there may indeed (still) be a mismatch. Maybe good noting<br>
that g_covar will also accept a .pdb file as reference. One way to be<br>
sure that things go right is to convert the .tpr to .pdb using the<br>
index with the group 'TDR':<br>
<br>
editconf -f topol.tpr -o TDR.pdb -n index.ndx<br>
<br>
Then use that file to convert the trajectory to .pdb:<br>
<br>
trjconv -s TDR.pdb -f traj.xtc -o traj.pdb<br>
<br>
You should be fine taking the system as the atoms should match now. To<br>
check if they do, visualize both topol.pdb and traj.pdb. You'll notice<br>
a mismatch by garbled atom types/names. You have to explicitly check<br>
for that. Such mismatches are a bit hard to spot, as the .xtc file<br>
does not contain atom metadata.<br>
<br>
Aside of that there is another possible cause for this error to occur,<br>
and that is when the system is split over the periodic boundaries.<br>
That will also break the routine, but will also immediately show up<br>
when visualizing the system as mentioned above.<br>
<br>
Then, by means of 'by the way', are you sure you want to use the -ref<br>
flag with g_covar? This means that the deviations are taken with<br>
respect to the reference coordinates rather than with respect to the<br>
average coordinates. This comes down to calculating a non-central<br>
second moment. To illustrate that, imagine tossing a dice to<br>
investigate the distribution of numbers. Fine, you come to an average<br>
and get the standard deviation the usual way. But what you do here is<br>
calculating the deviation from, say 5, rather than the average of 3.5,<br>
or worse even, from 8. Nice exercise to calculate the second moment<br>
you get in that case and to try and think of what it means. I don't<br>
say it has no meaning; in some cases it makes sense, but you'll have<br>
to have good reasons for doing it and justify the approach when it<br>
comes to publication. More so, it usually requires more thinking of<br>
what such results signify.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
<br>
2009/4/2 Dayle Smith <<a href="mailto:daylemariesmith@gmail.com">daylemariesmith@gmail.com</a>>:<br>
<div><div></div><div class="h5">> Thanks, Mark-<br>
> I re-ran a short MD simulation with TDR as the only xtc group, and used<br>
> tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar<br>
> with an index.ndx that contains only TPR (just to be safe!),<br>
><br>
> g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx<br>
><br>
> and I still get the Jacobi error:<br>
><br>
> Choose a group for the least squares fit<br>
> Group 0 ( TDR) has 29 elements<br>
> There is one group in the index<br>
><br>
> Choose a group for the covariance analysis<br>
> Group 0 ( TDR) has 29 elements<br>
> There is one group in the index<br>
> Calculating the average structure ...<br>
> Reading frame 0 time 0.000<br>
> -------------------------------------------------------<br>
> Program g_covar, VERSION 3.3.3<br>
> Source code file: nrjac.c, line: 129<br>
><br>
> Fatal error:<br>
> Error: Too many iterations in routine JACOBI<br>
><br>
> ~Dayle<br>
><br>
><br>
> On Wed, Apr 1, 2009 at 6:22 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> wrote:<br>
>><br>
>> Justin A. Lemkul wrote:<br>
>>><br>
>>><br>
>>> Dayle Smith wrote:<br>
>>>><br>
>>>> Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms<br>
>>>> in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is<br>
>>><br>
>>> Indeed, that's the problem, then!<br>
>>><br>
>>>> the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and<br>
>>>> now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I<br>
>>>> still can't get g_covar to work. Maybe these are unrelated problems, I'm not<br>
>>>> sure.<br>
>>><br>
>>> You haven't really changed anything. The xtc-grps parameter defines what<br>
>>> was saved in the simulation. Setting it after the fact does not affect the<br>
>>> already-produced .xtc file. What you need is a .tpr file that contains only<br>
>>> TDR, so you would have to make modifications to your .top in order to<br>
>>> generate this TDR-only .tpr file.<br>
>><br>
>> Or use tpbconv - this is the "other" application for that utility.<br>
>><br>
>> Mark<br>
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<br>
<br>
<br>
</div></div>--<br>
<div class="im">Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
</div>Padualaan 8<br>
3584 CH Utrecht<br>
<div class="im">The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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