MSD calculation

User discussions
1

GROMACS version: 2024.2
GROMACS modification: No

Hi everyone,

I have a simulation box containing TIP4P water and 30 solute molecules. I wanted to compute the MSD of the solutes. I tried:

gmx msd -f prod.xtc -s prod.tpr -o msd.xvg

But I get:

Requested tolerance cannot be achieved:
Frame 50 has non-integral time 0.100000. ‘gmx msd’ uses time discretization
internally and cannot work if the time (usually measured in ps) is not
integral. You can use ‘gmx convert-trj -dt 1’ to subsample your trajectory
before the analysis.

I don’t understand the error. Can someone explain? Thanks!

2

As far as I understand, this should be fixed in GROMACS 2025, see Allow femtosecond level trajectories to be analyzed in gmx-msd (!4428) · Merge requests · GROMACS / GROMACS · GitLab for some more information. Please, try the 2025-beta (from Downloads - GROMACS 2025.0-beta documentation) to see if it works for you.

3

Thank you! If I download the new version, can I analyze trajectories from the old version? I think it isn’t possible to analyze trajectories from the 2023 version with the 2024 version…

4

Yes, you should be able to analyze the results from GROMACS 2023 with GROMACS 2024. All GROMACS versions should be backwards compatible.

In this case, you may even need the 2025-beta version.