# Trajectory analysis in gromacs

**URL:** <https://gromacs.bioexcel.eu/t/trajectory-analysis-in-gromacs/835>\
**Category:** User discussions\
**Created:** [September 19, 2020, 12:13pm UTC](https://gromacs.bioexcel.eu/t/trajectory-analysis-in-gromacs/835 "2020-09-19T12:13:53Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [September 19, 2020, 12:13pm UTC](https://gromacs.bioexcel.eu/t/trajectory-analysis-in-gromacs/835/1 "2020-09-19T12:13:53Z")

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GROMACS version:  
GROMACS modification: No  
Dear all  
I want to do trajectory analyze for diffusion of a single water like this picture. unfortunately, I dont know how to do that. Can you please help me? what is the command for that to get trajectory like this.

thank you.

 ![Capture](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/723966fa6e7324000bdf6435fa4e5b00edb84e04.jpeg)

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 19, 2020, 3:36pm UTC](https://gromacs.bioexcel.eu/t/trajectory-analysis-in-gromacs/835/2 "2020-09-19T15:36:51Z")

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Extract coordinates with `gmx traj` and plot in whatever software allows you to do the 3D plots like this (gnuplot maybe?)

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<div class="post-metadata">

**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [September 19, 2020, 5:15pm UTC](https://gromacs.bioexcel.eu/t/trajectory-analysis-in-gromacs/835/3 "2020-09-19T17:15:29Z")

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Thank you Dr lemkul. I did it.