Regarding Principal Component Analysis (PCA)

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1

GROMACS version: 2019
GROMACS modification: Yes/No
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protein-SASA
protein-SASA3300×2550 681 KB

I have performed PCA analysis for Protein-ligand complex structure in Gromacs. I have plotted a 2D graph eigenvector1 VS eigenvector2 ( I have attached image Protein-SASA)

How to plot the Eigenvector Index graph? (as shown in the image eigenvector_Index)Eigenvector_index

Kindly share the steps and commands to plot the Eigenvector Index graph, it will be of great help! Thank you

2

Hi,
The file you are looking is eigenval.xvg. It is generated by gmx covar and you can plot it with xmgrace or with other plotting tools.
Best regards
Alessandra

3

@alevilla Thank you very much for your reply, I will surely check now