# MSD calculation for lithium ions

**URL:** <https://gromacs.bioexcel.eu/t/msd-calculation-for-lithium-ions/12796>\
**Category:** User discussions\
**Created:** [October 15, 2025, 3:41pm UTC](https://gromacs.bioexcel.eu/t/msd-calculation-for-lithium-ions/12796 "2025-10-15T15:41:01Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mdiazseg](https://avatars.discourse-cdn.com/v4/letter/m/c57346/32.png) [@mdiazseg](https://gromacs.bioexcel.eu/u/mdiazseg)\
**Post date:** [October 15, 2025, 3:41pm UTC](https://gromacs.bioexcel.eu/t/msd-calculation-for-lithium-ions/12796/1 "2025-10-15T15:41:01Z")

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Hello,

I am uncertain why when I do a msd calculation with gromacs I am obtaining the following strange results: I would appreciate a lot if someone could help me out please. Thank you! For example, the command I am using is gmx msd -f t550\_prodrun.xtc -s t550\_prodrun.tpr -o msd-Li.xvg

 ![image-1760542825405-gxaqg5mif](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/9bee720a7b4c89298acbc8d0b79312e952797c2a.png)

 ![image-1760542783873-lunxwaozu](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/178fa0df16fae1919677c29d8aafcd3cfc78dfbe.png)

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**Author:** ![costalt](https://avatars.discourse-cdn.com/v4/letter/c/977dab/32.png) [@costalt](https://gromacs.bioexcel.eu/u/costalt)\
**Post date:** [October 16, 2025, 2:33am UTC](https://gromacs.bioexcel.eu/t/msd-calculation-for-lithium-ions/12796/2 "2025-10-16T02:33:59Z")

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Dear @mdiazseg , please give us more details about the system and simulation you are running. What exactly is your issue?