Wrapping GROMACS by Python for me
Project description
gmxpy
Author: Goosang Yu
Contact: gsyu93@gmali.com
Wrapping GROMACS by python script for me
Since 2023. 07. 12.
Tested GROMCAS ver. 2023.1
You don need to use XMGRACE anymore!
GROMACS by default generates graphs of data in the form of xmgrace files (.xvg). Xmgrace produces visually appealing plots, but it can be cumbersome to handle in different languages or operating systems. The most important thing is that I am not familiar with it.
One of the functions included in gmxpy, called 'xvg2df', converts it into a much simpler DataFrame format.
import gmxpy as gmx
df_xvg = gmx.xvg2df('interaction_energy.xvg')
df_xvg()
| Coul-SR:Protein-JZ4 | LJ-SR:Protein-JZ4 | |
|---|---|---|
| Time (ps) | ||
| 0 | -15.2106 | -98.9382 |
| 10 | -15.5369 | -108.834 |
| 20 | -26.0345 | -105.193 |
| 30 | -13.2364 | -108.948 |
| 40 | -13.0772 | -109.427 |
With just a little additional effort, it can be conveniently plotted and visualized as a graph. I have freely chosen the colors that I personally like.
df_xvg().plot()
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