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

[Mark Abraham]

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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