Gmx msd standard library logic error

User discussions
1

GROMACS version: 2023.3
GROMACS modification: No

Hello,

i have a trajectory file with 0.2 picosecond timesteps. gmx msd does not work unless I put -dt 0.5, 1 or higher. I would like to be able to keep the resolution of the trajectory file. Any advice would be appreciated. Thank you!

This is the error message:

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

2

Hi!

Prior to GROMACS 2025, gmx msd cannot handle trajectories with <1 ps between frames (2023.4 has improved error reporting at least).

You can try GROMACS 2025-beta or wait a bit until 2025.0 is released in February.

P.S.: using -dt 0.5 with trajectory saved every 0.2 ps is a bad idea, even if it happens to work because of insufficient validity checking (should be improved in newer GROMASC versions).