[gmx-users] Segfaults with trjconv and g_dist

[Ondrej Marsalek]

I have just found that the problem (at least with trjconv) only
manifests if I include in the options "-pbc mol". I use a dodecahedron
box.

I will try to create a simple example that demonstrates this and post
it here, together with a script to create the whole thing.

Ondrej


On Mon, Nov 16, 2009 at 19:54, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
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