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
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