[gmx-users] Fatal error from grommp in gromacs 5.0.4

[Alexandr Nasedkin]

Hi James,

As a very quick check - did you do any editing of frame_2.gro?

It looks like you have an extra line or removed some line from gro-file.

If you manually edited it, beware of the total count of atoms in the 
very beginning of gro-file, which you should edit it as well.


More detailed information about commands you executed would also be 
helpful to solve the issue.


-Alexandr


On 23/12/2017 03:16, James wrote:
> Hi All,
>
> I've run into a perplexing problem. I take an initial .gro file, do an
> energy minimization on it, and then begin an MD simulation. File-wise, the
> sequence of events is:
>
> file_to_minimize.gro -> file_for_md.gro -> frame_1.gro -> frame_2.gro
>
> Everything is fine up until frame_2.gro, which is written with only 6 atom
> columns (the atom coordinates and velocities), whereas frame_1.gro had 9-10
> columns (residue number and name, and atom number and name, plus the other
> 6). The non-atom lines (title, atom count, and the last line for the
> bounding box) are fine. And, the atom columns that are present seem fine.
> The formats are as they should be, with no excessively large numbers or
> corruption.
>
> I'm not even sure the missing columns are the issue, so I guess the first
> question is: Should a .gro file work with only the atom coordinates and
> velocities (plus the appropriate header and footer lines)?
>
> Regardless, this is what I am getting when grommp tries to process
> frame_2.gro:
>
> ===============================
> gromacs-5.0.4/src/gromacs/fileio/confio.c, at line 1040:
>
> Fatal error:
> Something is wrong in the coordinate formatting of file
> frame_2.gro.
> ===============================
>
> In looking at confio.c, it seems that a line in frame_2.gro is failing the
> test at line 1038, which appears to be looking for 2 floating point numbers
> (why 2? I would think it would be 3, one each for X, Y, and Z). If it got
> that far (handling of the other columns occurs earlier in confio.c), that
> implies to me that perhaps the missing columns are not the issue. But if
> not, I don't know why its failing. And, either way, I don't know why the
> columns are missing.
>
> Has anyone seen this behavior before, or have a theory?
>
> By the way, in case any of the developers see this, an error that says
> "Something is wrong..." isn't all that informative (but better than
> nothing!). It would be great if sanity checks provided more information
> upon failure. In this case, knowing what line of the .gro file was causing
> the error, and printing the values for BUF, &x1, and &x2, would be really
> helpful. (That being said, I don't mean to sound too critical -- gromacs is
> a great tool and I realize there aren't enough resources to make everything
> perfect.)
>
> Sincerely,
> James