# Gromacs MSD

**URL:** <https://gromacs.bioexcel.eu/t/gromacs-msd/4436>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [July 7, 2022, 4:44pm UTC](https://gromacs.bioexcel.eu/t/gromacs-msd/4436 "2022-07-07T16:44:02Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Priya](https://avatars.discourse-cdn.com/v4/letter/p/eada6e/32.png) [@Priya](https://gromacs.bioexcel.eu/u/Priya)\
**Post date:** [July 7, 2022, 4:44pm UTC](https://gromacs.bioexcel.eu/t/gromacs-msd/4436/1 "2022-07-07T16:44:02Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

Hi,I want to calculate MSD - center of mass (COM) of a polymer system using gromacs.  
Can I know how to do that?

Regards,  
Priya

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**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\
**Post date:** [July 8, 2022, 2:26pm UTC](https://gromacs.bioexcel.eu/t/gromacs-msd/4436/2 "2022-07-08T14:26:17Z")

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GMX traj, option -com [gmx traj — GROMACS 2020-beta2 documentation](https://manual.gromacs.org/documentation/2020-beta2/onlinehelp/gmx-traj.html)  
For example for center of mass for my ring in polar head in my lipid for z coordinates I used for one frame  
gmx traj -f eq1\_merged\_dt\_100.xtc -s eq3.tpr -n dgdg\_rings.ndx -com -nox -noy -ox dgdg\_com\_bottom\_$number.xvg -b 100000 -e 100000

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**Author:** ![Priya](https://avatars.discourse-cdn.com/v4/letter/p/eada6e/32.png) [@Priya](https://gromacs.bioexcel.eu/u/Priya)\
**Post date:** [July 15, 2022, 10:32pm UTC](https://gromacs.bioexcel.eu/t/gromacs-msd/4436/3 "2022-07-15T22:32:30Z")

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Thanks,  
Do you know how to create ndx files?

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**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\
**Post date:** [July 16, 2022, 12:24am UTC](https://gromacs.bioexcel.eu/t/gromacs-msd/4436/4 "2022-07-16T00:24:20Z")

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Yeah sure. You need use gmx make\_ndx [gmx make\_ndx — GROMACS 2022.2 documentation](https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html)

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**Author:** ![Priya](https://avatars.discourse-cdn.com/v4/letter/p/eada6e/32.png) [@Priya](https://gromacs.bioexcel.eu/u/Priya)\
**Post date:** [July 17, 2022, 3:42pm UTC](https://gromacs.bioexcel.eu/t/gromacs-msd/4436/5 "2022-07-17T15:42:10Z")

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Thank you