[gmx-users] inexplicable rmsf error - Too many iterations in routine JACOBI

[Mala L Radhakrishnan]

Hi,

..just as a follow up with more information:

When I use gmx trajconv to extract snapshots that contain only the molecule
of interest from my original "full" .xtc file,  for my RMSF calculation,
(using the same index as before) and then use gmx rmsf -f traj.pdb instead
of on the traj.xtc, it works fine.  So there is some reason that using the
.xtc file leads to this error, and only when my reference structure
contains only the molecule of interest.  Is there an explanation for why
I'm seeing this bug?  Is my .xtc file somehow corrupted in a weird way?  Or
is it likely fine but gmx rmsf is finicky and so using the .pdb trajectory,
so long as it works, is fine, and this bug shouldn't indicate an issue with
my .xtc file?

Thanks for any info...

Mala

On Fri, Jul 19, 2019 at 5:28 AM Mala L Radhakrishnan <mradhakr at wellesley.edu>
wrote:

> Hi all,
>
> I am trying to run gmx RMSF using.a particular snapshot as my reference
> structure (-s option).
>
> When I extract a gro file to make my reference structure that has only the
> molecule that INCLUDES the alpha-carbons in my index file that I want to
> use for my RMSF calculation (I checked), then midway through its reading in
> the frames (and not always at the same point) I get the following error:
>
> Program:     gmx rmsf, version 2016.3
> Source file: src/gromacs/linearalgebra/nrjac.cpp (line 165)
>
> Fatal error:
> Error: Too many iterations in routine JACOBI
>
> When I extract a gro file that has an even larger subset of the atoms in
> the frame than the one requested previously, it seg-faults right away.
>
> But when I extract a snapshot that has the *entire* system to use as my
> reference structure (all atoms, including solvent and ions), it seems to
> work. I am using the same .xtc file and index file in all cases, just
> changing the -s file.
>
> Googling the error suggests that I have a mismatch somewhere in my index
> file and/or structure file, but (a) I have checked this by eye and can't
> find any mismatches and (b) when I do he same sort of extraction of a
> subset of the system on several other trajectories it works just fine -- in
> other words, this seems to be the only trajectory where I need to extract
> the entire system (including solvent, ions, etc.) as my reference frame
> just to get an rmsf of alpha carbons in the protein molecule of interest. I
> am using version 2016.3.  I have tried multiple gromacs versions to extract
> and run just in case but got the same error.  The reference structure also
> appears to be structurally fine (no broken molecules, etc.)
>
> What could be different about this trajectory that is causing the problem?
> Again, I looked by eye at the gro file I'm using as my reference structure
> and made sure that it contains all the atoms in the index file selection
> I'm using for my RMSF calculation...
>
> Thanks for any help. I am happy to send you the files for which it works
> and for which it doesn't...just very confused!
>
> Mala
>
>
>
> --
> Mala L. Radhakrishnan
> Associate Professor of Chemistry
> Director, Biochemistry Program
> Wellesley College
> 106 Central Street
> Wellesley, MA 02481
> (781)283-2981
>


-- 
Mala L. Radhakrishnan
Associate Professor of Chemistry
Director, Biochemistry Program
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981