# MSD calculation

**URL:** <https://gromacs.bioexcel.eu/t/msd-calculation/10626>\
**Category:** User discussions\
**Created:** [November 25, 2024, 1:19pm UTC](https://gromacs.bioexcel.eu/t/msd-calculation/10626 "2024-11-25T13:19:40Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![horlust](https://avatars.discourse-cdn.com/v4/letter/h/b2d939/32.png) [@horlust](https://gromacs.bioexcel.eu/u/horlust)\
**Post date:** [November 25, 2024, 1:19pm UTC](https://gromacs.bioexcel.eu/t/msd-calculation/10626/1 "2024-11-25T13:19:40Z")

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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!

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 25, 2024, 3:03pm UTC](https://gromacs.bioexcel.eu/t/msd-calculation/10626/2 "2024-11-25T15:03:34Z")

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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](https://gitlab.com/gromacs/gromacs/-/merge_requests/4428) for some more information. Please, try the 2025-beta (from [Downloads - GROMACS 2025.0-beta documentation](https://manual.gromacs.org/2025.0-beta/download.html)) to see if it works for you.

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<div class="post-metadata">

**Author:** ![horlust](https://avatars.discourse-cdn.com/v4/letter/h/b2d939/32.png) [@horlust](https://gromacs.bioexcel.eu/u/horlust)\
**Post date:** [November 26, 2024, 7:41am UTC](https://gromacs.bioexcel.eu/t/msd-calculation/10626/3 "2024-11-26T07:41:30Z")

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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…

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<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 26, 2024, 8:05am UTC](https://gromacs.bioexcel.eu/t/msd-calculation/10626/4 "2024-11-26T08:05:33Z")

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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.