# Analysis from output
**URL:** https://gromacs.bioexcel.eu/t/analysis-from-output/5751
**Category:** User discussions
**Created:** [February 7, 2023, 5:03pm UTC](https://gromacs.bioexcel.eu/t/analysis-from-output/5751 "2023-02-07T17:03:04Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@blablablablablablab](https://gromacs.bioexcel.eu/u/blablablablablablab)
#### Post date: [February 7, 2023, 5:03pm UTC](https://gromacs.bioexcel.eu/t/analysis-from-output/5751/1 "2023-02-07T17:03:05Z")
GROMACS version: 2020.4
GROMACS modification: Yes
Here post your question : I have a protein with 5 domains and a dsDNA . I want to calculate the angles and distances between centers of masses of the domains and DNA. Do I make indexes of all the domains from the output files of the simulation and then use gmx distance ? or this will be easier with MD analysis? A workflow would be highly appreciated.
---
### Author:  [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)
#### Post date: [February 21, 2023, 9:36am UTC](https://gromacs.bioexcel.eu/t/analysis-from-output/5751/2 "2023-02-21T09:36:46Z")
Hi,
I understood that you what to calculate the distance between com of the DNA and com of each protein domain, then you can also use gmx pairdist see [https://manual.gromacs.org/current/onlinehelp/gmx-pairdist.html](https://manual.gromacs.org/current/onlinehelp/gmx-pairdist.html)
\Alessandra
---
### Author:  [@blablablablablablab](https://gromacs.bioexcel.eu/u/blablablablablablab)
#### Post date: [February 21, 2023, 4:41pm UTC](https://gromacs.bioexcel.eu/t/analysis-from-output/5751/3 "2023-02-21T16:41:41Z")
Hi Madam, are the MD analysis scripts for angle between the domains and Center of mass more helpful in terms of plotting the data and working with them?