PCA analysis for protein alone and complex(protein_ligand)

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GROMACS version: 2023.3
GROMACS modification: Yes/No
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Dear All,

Am completed MD Simulations for protein alone and complexes(protein_ligand) and Now i need PCA analysis for both protein alone and Complexes. Can you please me for find the

  1. What are the commands required for PCA analysis?

  2. How to extract PC1, PC2 and PC3 and how to anlayse the variance between PC1 & PC2 and PC2 & PC3 and PC3 & PC1 in percentage?

  3. Finally how to get scattered plots for all the three PC’s ?

I need scattered plots like this
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