[gmx-users] Re: Segfaults with trjconv and g_dist

[Ondrej Marsalek]

Happens with a single frame in a gro file as well, for example in this
simple case:

1) take a gro file for the full system
2) use trjconv to save a subset of the system in a new gro file
3) create and index file for that
4) try to use g_dist on the index file from 3) and gro file from 2)
5) enjoy segfault

Does anyone else see this, or am I doing something wrong? Will be
happy to post more details if needed.

Ondrej


On Mon, Nov 16, 2009 at 18:22, Ondrej Marsalek
<ondrej.marsalek at gmail.com> wrote:
> Dear all,
>
> as a quick check, before I dive deeper, I would like to ask the following.
>
> I have a simulation (protein in water and counterions) for which I
> have defined an xtc output group (protein and conunterions). If I try
> to run trjconv or g_dist over this xtc file (and a proper reduced
> index file), I get a segmentation fault. I also get this if I filter
> out water from the full trr file and try to process the rest. If I use
> the original trr file for g_dist or trjconv, it works just fine.
> Before I try to resolve this, I'd like to know if anyone has
> encountered anything like this. Tested on 4.0.4 and 4.0.5.
>
> In case this will need a bug report - are tpr files portable, is it OK
> to attach one to a bug report?
>
> Thanks,
> Ondrej
>