[gmx-users] Segfaults with trjconv and g_dist

[Tsjerk Wassenaar]

Hi Ondrej,

Please paste the exact series of commands you used. That will make it
easier to indicate where errors are being introduced.

Cheers,

Tsjerk

On Mon, Nov 16, 2009 at 6:53 PM, Ondrej Marsalek
<ondrej.marsalek at gmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist