gmx convert-tpr segmentation fault
Summary I tried using gmx convert-tpr to write a new tpr for the protein index group, which resulted in a segfault. This happens in the 2023 and 2024 GROMACS versions.
**GROMACS VERSION** 2023.4/2024.1
**Error** gmx convert-tpr -s em.tpr -n protein.ndx -o protein.tpr :-) GROMACS - gmx convert-tpr, 2023.4 (-:
Executable: /opt/apps/gromacs/2023.4/bin/gmx
Data prefix: /opt/apps/gromacs/2023.4
Working dir: /home/vasista/$USER/simulations/files_with_2023_gromacs
Command line: gmx convert-tpr -s em.tpr -n protein.ndx -o protein.tpr
Reading file em.tpr, VERSION 2023.4 (single precision)
Group 0 ( System) has 1862171 elements Group 1 ( Protein) has 49140 elements Group 2 ( Protein-H) has 25980 elements Group 3 ( C-alpha) has 2880 elements Group 4 ( Backbone) has 8640 elements Group 5 ( MainChain) has 11460 elements Group 6 ( MainChain+Cb) has 14340 elements Group 7 ( MainChain+H) has 14460 elements Group 8 ( SideChain) has 34680 elements Group 9 ( SideChain-H) has 14520 elements Group 10 ( Prot-Masses) has 49140 elements Group 11 ( non-Protein) has 1813031 elements Group 12 ( Water) has 1810731 elements Group 13 ( SOL) has 1810731 elements Group 14 ( non-Water) has 51440 elements Group 15 ( Ion) has 2300 elements Group 16 ( Water_and_ions) has 1813031 elements Group 17 ( Protein) has 49140 elements
Select a group: 1
Selected 1: 'Protein'
Will write subset Protein of original tpx containing 49140 atoms
\[mm51:10752\] \*\*\* Process received signal \*\*\*
\[mm51:10752\] Signal: Segmentation fault (11)
\[mm51:10752\] Signal code: Address not mapped (1)
\[mm51:10752\] Failing at address: (nil)
\[mm51:10752\] \[ 0\] /lib64/libpthread.so.0(+0xf630)\[0x7f209ed47630\]
\[mm51:10752\] \[ 1\] /opt/apps/gromacs/2023.4/lib64/libgromacs.so.8(+0x97f80e)\[0x7f209fe5680e\]
\[mm51:10752\] \[ 2\] /opt/apps/gromacs/2023.4/lib64/libgromacs.so.8(+0x981a88)\[0x7f209fe58a88\]
\[mm51:10752\] \[ 3\] /opt/apps/gromacs/2023.4/lib64/libgromacs.so.8(+0x47ebec)\[0x7f209f955bec\]
\[mm51:10752\] \[ 4\] /opt/apps/gromacs/2023.4/lib64/libgromacs.so.8(\_ZN3gmx24CommandLineModuleManager3runEiPPc+0x305)\[0x7f209f953df5\]
\[mm51:10752\] \[ 5\] gmx\[0x40570d\]
\[mm51:10752\] \[ 6\] /lib64/libc.so.6(\__libc_start_main+0xf5)\[0x7f209e098555\]
\[mm51:10752\] \[ 7\] gmx\[0x405774\] \[mm51:10752\]
\*\*\* End of error message \*\*\* Segmentation fault
Steps to reproduce
gmx convert-tpr -s em.tpr -n protein.ndx -o protein.tpr
What is the current bug behavior?
Segmentation fault
What did you expect the correct behavior to be?
Produce a tpr file for the given selection group.
Possible fixes
Files
Edited by Mark Abraham