# How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-calculate-ligand-active-site-distance-in-a-ligand-protein-complex-from-md-simulation/1654>\
**Category:** User discussions\
**Created:** [February 28, 2021, 2:22pm UTC](https://gromacs.bioexcel.eu/t/how-to-calculate-ligand-active-site-distance-in-a-ligand-protein-complex-from-md-simulation/1654 "2021-02-28T14:22:12Z")\
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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:** [March 8, 2021, 4:23pm UTC](https://gromacs.bioexcel.eu/t/how-to-calculate-ligand-active-site-distance-in-a-ligand-protein-complex-from-md-simulation/1654/2 "2021-03-08T16:23:16Z")

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Hi,  
a variety of tools are available in GROMACS to calculate distance.  
Maybe you can find some help from this conversation

> [@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.

Or other in the forum.  
Best regards  
Alessandra

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