[gmx-users] Segfaults with trjconv and g_dist

[Ondrej Marsalek]

Hi Tsjerk,

this is the kind of problem that I was expecting, but though that it
could be resolved by providing a custom index file that uses numbering
that corresponds to the reduced file. This, however, does not seem to
work for me. Even when use pass (using -n) and index file (created
based on the reduced file) that uses only indices within the range
present in the reduced file, it still crashes. Using wrong index file
(with indices from the full configuration) indeed fails, but with a
nice error message.

As a side note, it would be nice to avoid segfaults in general, even
with wrong user input.

Ondrej


On Mon, Nov 16, 2009 at 18:38, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Ondrej,
>
> This is not a bug, but arises from the inconsistency of the .tpr file
> and the .xtc file. g_dist uses an internal index group derived from
> the .tpr file. But that file contains more atoms than the trajectory
> file, and some index numbers for counterions are higher than the
> highest entry in the frame from the trajectory. Hence, you get a
> segmentation fault. If you create an index group yourself from the
> .tpr file, you have the same issue. To avoid it, you can create a
> coordinate file from the .tpr matching the atoms in the .xtc file.
>
> Hope it helps,
>
> Tsjerk
>
> On Mon, Nov 16, 2009 at 6:22 PM, 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
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
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