[gmx-users] Segfaults with trjconv and g_dist

[Ondrej Marsalek]

Unfortunately, it is not straightforward to isolate the issue
completely. So far, I have the following, extracted from the original
data of interest. In the directory test that can be found here:

http://www.molecular.cz/~marsalek/tmp/test.tar.bz2

if I run these two commands:

echo 3 8 | g_dist -f conf-protein.gro -s topol.tpr -n index.ndx
echo 3 8 | g_dist -f conf-protein-ions.gro -s topol.tpr -n index.ndx

I get normal output in the first case and a segfault in the second.
The two configurations are extracted from the full configuration - one
is only "protein" and the other is "protein" and counterions.

Any help or pointers appreciated,
Ondrej


On Mon, Nov 16, 2009 at 19:58, Ondrej Marsalek
<ondrej.marsalek at gmail.com> wrote:
> 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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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>