Standard library logic error (bug): (exception type: St12length_error) vector::_M_default_append

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Command line:
gmx trjconv -s fnIII-12_SAMoh_T298.tpr -f traj_comp.xtc -o fnIII-12_SAMoh_T298-10.xtc -pbc mol -skip 10

Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file fnIII-12_SAMoh_T298.tpr, VERSION 2023.3-EasyBuild_4.8.0 (double precision)
Reading file fnIII-12_SAMoh_T298.tpr, VERSION 2023.3-EasyBuild_4.8.0 (double precision)

Program: gmx trjconv, version 2021.4-Ubuntu-2021.4-2

Standard library logic error (bug):
(exception type: St12length_error)
vector::_M_default_append

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

Do I understand it correctly, that you are trying to use gmx trjconv version 2021.4 with a tpr file generated using GROMACS version 2023.3? If so, see if it helps using a more recent version to run gmx trjconv. GROMACS can read tpr files generated by older versions (backwards compatible), but not necessarily tpr files from more recent versions of GROMACS - that may or may not work.

3

I tried to run following command to generate every 10th frame of my xtc file
gmx trjconv -s fnIII-12_SAMoh_T298.tpr -f traj_comp.xtc -o fnIII-12_SAMoh_T298-10.xtc -pbc mol -skip 10

In return I got this message on screen,
Program: gmx trjconv, version 2021.4-Ubuntu-2021.4-2

Standard library logic error (bug):
(exception type: St12length_error)
vector::_M_default_append

Earlier I used to do with same ubuntu version and gromacs updated version and it worked but this time it is showing above mentioned error!

4

Was it the same tpr file when it worked before? You said that it worked with “gromacs updated version”. Was that by any chance a 2023 (or later) version?

As I said, 2021.4 will almost certainly not work with a tpr file from 2023.3. If you upgrade to 2023, or even better 2024, I’m reasonably certain it will work.

5

Hi,
I was able to work on it. Thank you.