# Regarding gmx distance

**URL:** <https://gromacs.bioexcel.eu/t/regarding-gmx-distance/2264>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [June 1, 2021, 6:51am UTC](https://gromacs.bioexcel.eu/t/regarding-gmx-distance/2264 "2021-06-01T06:51:28Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ikuma](https://avatars.discourse-cdn.com/v4/letter/i/a4c791/32.png) [@ikuma](https://gromacs.bioexcel.eu/u/ikuma)\
**Post date:** [June 1, 2021, 6:51am UTC](https://gromacs.bioexcel.eu/t/regarding-gmx-distance/2264/1 "2021-06-01T06:51:28Z")

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GROMACS version:2020.2  
GROMACS modification: Yes  
Dear users,

I’d like to calculate distance between a center of mass on molecule and specific 3d coordinate in my simulation box(e.g. center of PBC).  
Can I calculate it with gmx distance? As far as I understand, gmx distance calculate distance between a pair of atom or group, not distance between specific coordinate and a group.

Best,  
Kimu

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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:** [June 11, 2021, 12:20pm UTC](https://gromacs.bioexcel.eu/t/regarding-gmx-distance/2264/2 "2021-06-11T12:20:52Z")

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Hi,  
here you can find the difference between gromacs tools that calculate distance. I hope it help to find the best tool

> [@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):
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> 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.

\Alessandra

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**Author:** ![ikuma](https://avatars.discourse-cdn.com/v4/letter/i/a4c791/32.png) [@ikuma](https://gromacs.bioexcel.eu/u/ikuma)\
**Post date:** [June 14, 2021, 12:35am UTC](https://gromacs.bioexcel.eu/t/regarding-gmx-distance/2264/3 "2021-06-14T00:35:27Z")

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Hi Alessandra,  
thank you for your reply.  
I’ll check it.

Best Regards,  
Kimu