[gmx-users] A debugger to detect the reason of segmentation fault of Gromacs

[Hoa Trinh]

Dear Mark,
I am working on a project which requires me to modify the source code of
Gromacs to include a potential energy which Gromacs doesn't have. The
segmentation fault happens immediately at the first step of minimization
with Gromacs 5.0.7 and the force was reported to be 0. My system is just a
coarse-grained of protein which contains ~ 100 beads in the vacuum, I
already tested it with the modifed source code of Gromacs version 4 and it
works just fine. As a novice, I might have done something wrong with the
source code.
 As you said, gdb is not much of help but I think it worths a try. Thank
you.

*Lan Hoa*

2017-10-14 13:16 GMT-05:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Anything is fine, e.g. gdb is widely available. But you are unlikely to
> learn anything actionable. Most people's segfaults are because of one of
> the cases of http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> because
> their model and/or their starting configuration are somehow not
> appropriate. Why do you think your case might be different?
>
> Mark
>
> On Sat, Oct 14, 2017 at 7:16 PM Hoa Trinh <trinhlanhoa at gmail.com> wrote:
>
> > Hi,
> > Can anyone please recommend debuggers to detect the reason of
> segmentation
> > fault of Gromacs?
> > Thank you very much in advance.
> > Best,
> > *Lan Hoa*
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