# 3D Gibbs free energy landscape

**URL:** <https://gromacs.bioexcel.eu/t/3d-gibbs-free-energy-landscape/1424>\
**Category:** User discussions\
**Created:** [January 12, 2021, 10:02am UTC](https://gromacs.bioexcel.eu/t/3d-gibbs-free-energy-landscape/1424 "2021-01-12T10:02:42Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![shailesh](https://avatars.discourse-cdn.com/v4/letter/s/50afbb/32.png) [@shailesh](https://gromacs.bioexcel.eu/u/shailesh)\
**Post date:** [January 12, 2021, 10:02am UTC](https://gromacs.bioexcel.eu/t/3d-gibbs-free-energy-landscape/1424/1 "2021-01-12T10:02:42Z")

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GROMACS version:2020.1  
GROMACS modification: No

Sir i want to generate 3D Gibbs free energy landscape plot using gromacs.  
please provide me gromacs command , so that i can generate the 3D plot

thankyou  
With Regards  
Shailesh Mani Tripathi  
Central University of Rajasthan

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [January 12, 2021, 3:15pm UTC](https://gromacs.bioexcel.eu/t/3d-gibbs-free-energy-landscape/1424/2 "2021-01-12T15:15:39Z")

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HI Shailesh,

It’s hard to help you, because there is no universal 3D Gibbs free energy landscape.

To generate such a landscape, you would have to say what want to be looking at, e.g., a distance, an angle, or projections onto principal components.

Once you determined what the essential observables of your system are, you would calculate them frame-by-frame from your simulation – imagine a table like this:

| frame | distance C\_1 - N\_2 | another distance | projection on principal compent 1 |
| --- | --- | --- | --- |
| 1 | 0.22 | 0.13 | 0.54 |
| … | … | … | … |
| 10 000 | 0.21 | 0.03 | -0.9 |

Then, you can use some type of density estimation tool to plot the three-dimensional density. For this, I would rather suggest some combination of python tools (especially matplotlib, pandas and seaborn are helpful here) than the built in GROMACS tools.