# COnfusion on Implimentation of pairdist and rms

**URL:** <https://gromacs.bioexcel.eu/t/confusion-on-implimentation-of-pairdist-and-rms/7595>\
**Category:** User discussions\
**Tags:** gmx-pairdist\
**Created:** [November 9, 2023, 2:04pm UTC](https://gromacs.bioexcel.eu/t/confusion-on-implimentation-of-pairdist-and-rms/7595 "2023-11-09T14:04:06Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Ben\_Allott](https://avatars.discourse-cdn.com/v4/letter/b/f0a364/32.png) [@Ben\_Allott](https://gromacs.bioexcel.eu/u/Ben_Allott)\
**Post date:** [November 9, 2023, 2:04pm UTC](https://gromacs.bioexcel.eu/t/confusion-on-implimentation-of-pairdist-and-rms/7595/1 "2023-11-09T14:04:06Z")

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GROMACS version: GROMACS/2021.3-foss-2021a  
GROMACS modification: Yes/No

Hey There,

I’m reaching out for guidance on generating an RMSD plot using GROMACS for my PhD research. Specifically, I need to analyse a molecule’s insertion into DNA over the entire trajectory. My initial attempt with `gmx rms` compared the molecule’s trajectory positions to a single reference position of the DNA insertion site, rather than to corresponding frames throughout the trajectory.

Could you advise whether there’s a method to plot RMSD by comparing the positions of the molecule and the DNA insertion site across each frame of the trajectory?

Additionally, I have experimented with `gmx pairdist` and obtained a promising graph. However, I am uncertain if it reflects the center of mass for both groups. Would adding the `-selpos mol_com` option calculate the center of mass for both the molecule and the DNA insertion site?

Your prompt assistance would be greatly beneficial as I am approaching the deadline of my doctoral program.

many thanks in advance,

Ben