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
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.