# End to end polymer distance calculation

**URL:** <https://gromacs.bioexcel.eu/t/end-to-end-polymer-distance-calculation/1998>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [April 21, 2021, 4:50am UTC](https://gromacs.bioexcel.eu/t/end-to-end-polymer-distance-calculation/1998 "2021-04-21T04:50:34Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [April 22, 2021, 10:06am UTC](https://gromacs.bioexcel.eu/t/end-to-end-polymer-distance-calculation/1998/2 "2021-04-22T10:06:13Z")

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HI,  
you can generate an index file and the use gmx distance. This post may help you

> [@Using gmx distance to calculate end-to-end distance between polymeric chains](https://gromacs.bioexcel.eu/t/using-gmx-distance-to-calculate-end-to-end-distance-between-polymeric-chains/1712):
>
> GROMACS version: 2018.4 GROMACS modification: No Here post your question: I am trying to calculate the time averaged end-to-end distance of polymeric chains. I have 128 chains in my system and I want to compute an average end-to-end distance of these 128 chains as a function of time. I tried using an index file containing pairs of initial and final atom as follows: [Index] 1 10 11 20 21 30 … where 1, 10, … represent initial and final atom no of a single chain. I am not sure whether this…

In general for the difference between

> [@Tinto.Alencherry](#):
>
> gmx distance, gmx mindist or gmx pairdist

you can look to the following post

> [@What is the difference between gmx distance, gmx mindist and gmx pairdist?](https://gromacs.bioexcel.eu/t/what-is-the-difference-between-gmx-distance-gmx-mindist-and-gmx-pairdist/649):
>
> Hi, I am trying to compute distance between four residues of a protein involved in active site. I am getting confused in mindist, pairdist and gmx distance. What are the limits and differences in three? Which analysis can be helpful in plotting distance between A-B, B-C, C-D and D-A residues over time, where ABCD are 4 residues forming bottleneck for ligand entry.

Best regards  
Alessandra

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