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

[Peter Kroon]

Hi all,

I'm trying to produce a tng file from my trajectory (can mdrun write
those directly yet?) 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? 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 (-:

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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)