Standard library logic error in GMX MSD

User discussions
1

GROMACS version: 2023
GROMACS modification: No

Hello all,

I am attempting to calculate the mean square displacement for a single molecule in a cubic waterbox (4.5 nm side length). When running gmx msd, I get a standard library logic error:

>$ gmx msd -f bulk_md.trr -s bulk_md.tpr -o bulk_md_msd.xvg -n bulk.ndx

                    :-) GROMACS - gmx msd, 2023 (-:

Executable: /usr/local/gromacs-2023/bin/gmx
Data prefix: /usr/local/gromacs-2023
Working dir: /mnt/3a29b482-dac1-4563-be89-d63ad92354e9/membrane_permeation/solutes/BRIBP
Command line:
gmx msd -f bulk_md.trr -s bulk_md.tpr -o bulk_md_msd.xvg -n bulk.ndx

Available static index groups:
Group 0 “System” (9376 atoms)
Group 1 “LIG” (20 atoms)
Group 2 “BRI” (20 atoms)
Group 3 “NA” (1 atoms)
Group 4 “CL” (1 atoms)
Group 5 “Water” (9354 atoms)
Group 6 “SOL” (9354 atoms)
Group 7 “non-Water” (22 atoms)
Group 8 “Ion” (2 atoms)
Group 9 “Water_and_ions” (9356 atoms)
Specify any number of selections for option ‘sel’
(Selections to compute MSDs for from the reference):
(one per line, for status/groups, ‘help’ for help, Ctrl-D to end)

1
Selection ‘1’ parsed
Reading file bulk_md.tpr, VERSION 2023 (single precision)
Reading file bulk_md.tpr, VERSION 2023 (single precision)
trr version: GMX_trn_file (single precision)
Reading frame 1 time 0.001

Program: gmx msd, version 2023

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

I am able to parse the tpr and trr files with gmx velacc, so I’m confident the files are not corrupted.

Could anyone suggest what might be causing this error?

2

Hi,

One possibility is that your trajectory is saved with sub-picosecond frequency. gmx msd cannot handle such inputs in GROMACS 2023.

GROMACS 2023.4 and newer produce a proper warning, and GROMACS 2025.0 and newer can process such trajectories fine.

Please try with a newer GROMACS version. If you still see the problem with GROMACS 2025.3, please share a small sample of your trajectory so that we can reproduce and debug the issue.