[gmx-users] gmx trjconv to produce tng produces segfault

[Peter Kroon]

Thanks Mark. I added my files and description to
https://redmine.gromacs.org/issues/2187.


Peter


On 12-10-17 12:02, Mark Abraham wrote:
> Hi,
>
> On Thu, Oct 12, 2017 at 11:26 AM Peter Kroon <p.c.kroon at rug.nl> wrote:
>
>> Hi all,
>>
>> I'm trying to produce a tng file from my trajectory (can mdrun write
>> those directly yet?)
>
> gmx mdrun -x file.tng has always worked, but we can't make that the default
> until we've got more things working well in the broader infrastructure.
>
>
>> since VMD likes those better for coarse grained
>> systems. I'm not interested in my solvent, so I select a smaller group
>> for my output.
>>
>> When I run the following commands it produces a segfault. If I tell it
>> to output group "System" instead of "macro" it does work as expected. Is
>> this a known issue or should I report it somewhere?
>
> There are some TNG-related subset issues reported on
> https://redmine.gromacs.org that we have not yet had time to deal with, but
> a further report, and or confirmation is most welcome, particular with
> inputs that reproduce the problem.
>
> Mark
>
> I get the same
>> behaviour on GMX 5.1.4
>>
>> $ source /usr/local/gromacs-2016.3/bin/GMXRC
>>
>> $ gmx trjconv -f run.xtc -s run.tpr -o run.tng -center -n index.ndx -pbc
>> whole
>>                      :-) GROMACS - gmx trjconv, 2016.3 (-:
>>
>>                             GROMACS is written by:
>>      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
>> Bjelkmar
>>  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof
>>  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios
>> Karkoulis
>>     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
>>   Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik Marklund
>>    Teemu Murtola       Szilard Pall       Sander Pronk      Roland Schulz
>>   Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter Tieleman
>>   Teemu Virolainen  Christian Wennberg    Maarten Wolf
>>                            and the project leaders:
>>         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2017, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> GROMACS:      gmx trjconv, version 2016.3
>> Executable:   /usr/local/gromacs-2016.3/bin/gmx
>> Data prefix:  /usr/local/gromacs-2016.3
>> Working dir:  /coarse/peterkroon/DCL/Martini/fiber_daft/6-macro-1
>> Command line:
>>   gmx trjconv -f run.xtc -s run.tpr -o run.tng -center -n index.ndx -pbc
>> whole
>>
>> Will write tng: Trajectory file (tng format)
>> Reading file run.tpr, VERSION 5.1.4 (single precision)
>> Reading file run.tpr, VERSION 5.1.4 (single precision)
>> Reading file run.tpr, VERSION 5.1.4 (single precision)
>> Select group for centering
>> Group     0 (         System) has  2792 elements
>> Group     1 (          Other) has  2714 elements
>> Group     2 (            DTB) has    18 elements
>> Group     3 (              W) has  2696 elements
>> Group     4 (        Protein) has    78 elements
>> Group     5 (      Protein-H) has    78 elements
>> Group     6 (        C-alpha) has     0 elements
>> Group     7 (       Backbone) has     0 elements
>> Group     8 (      MainChain) has     0 elements
>> Group     9 (   MainChain+Cb) has     0 elements
>> Group    10 (    MainChain+H) has     0 elements
>> Group    11 (      SideChain) has    78 elements
>> Group    12 (    SideChain-H) has    78 elements
>> Group    13 (    Prot-Masses) has    78 elements
>> Group    14 (    non-Protein) has  2714 elements
>> Group    15 (          macro) has    96 elements
>> Group    16 (        Solvent) has  2696 elements
>> Select a group: 2
>> Selected 2: 'DTB'
>> Select group for output
>> Group     0 (         System) has  2792 elements
>> Group     1 (          Other) has  2714 elements
>> Group     2 (            DTB) has    18 elements
>> Group     3 (              W) has  2696 elements
>> Group     4 (        Protein) has    78 elements
>> Group     5 (      Protein-H) has    78 elements
>> Group     6 (        C-alpha) has     0 elements
>> Group     7 (       Backbone) has     0 elements
>> Group     8 (      MainChain) has     0 elements
>> Group     9 (   MainChain+Cb) has     0 elements
>> Group    10 (    MainChain+H) has     0 elements
>> Group    11 (      SideChain) has    78 elements
>> Group    12 (    SideChain-H) has    78 elements
>> Group    13 (    Prot-Masses) has    78 elements
>> Group    14 (    non-Protein) has  2714 elements
>> Group    15 (          macro) has    96 elements
>> Group    16 (        Solvent) has  2696 elements
>> Select a group: 15
>> Selected 15: 'macro'
>> Reading frame       0 time    0.000
>> Precision of run.xtc is 0.01 (nm)
>>
>> Back Off! I just backed up run.tng to ./#run.tng.1#
>> Segmentation fault (core dumped)
>>
>>
>> --
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