You can use the following scheme as a guide:-

1. Do the RMSD first

2. Then do the RMSF calculations.

3. Do the PCA. If you want, study the theory of Normal Mode Analysis and do the calculations.

4. There comes one of my favourite tools, g_mmpbsa. Go to the site and study the installation and usage, it will give you the energy contributions of residues.

5. H-bond analyses.

6. For a protein-ligand system, you can do Umbrella sampling to find out the delG value. And from that you can forward your calculations.

7. Plot a contact matrix.

Good luck...

Follow this review

Article Available Instruments for Analyzing Molecular Dynamics Trajectories

MD analysis depend on your simulation system. If you are considering protein, just follow the link: http://www.drugdesign.gr/uploads/7/6/0/2/7602318/lecture_mdanalysis.pdf

https://hpc-forge.cineca.it/files/CoursesDev/public/2015/High_Performance_Molecular_Dynamics/Rome/February/Tutorial4_Analysis.pdf

The type of analysis depends on your simulation system, plus the objective of your study. Usually, the RMSD and RMSF plots are drawn, however, each of the Rg, SASA, H-bonds, secondary structures, PCA, free energies and many other analyses is adopted based on what information you intend to derive from your simulation.

You can use the following scheme as a guide:-

1. Do the RMSD first

2. Then do the RMSF calculations.

3. Do the PCA. If you want, study the theory of Normal Mode Analysis and do the calculations.

4. There comes one of my favourite tools, g_mmpbsa. Go to the site and study the installation and usage, it will give you the energy contributions of residues.

5. H-bond analyses.

6. For a protein-ligand system, you can do Umbrella sampling to find out the delG value. And from that you can forward your calculations.

7. Plot a contact matrix.

Good luck...

The attachment was helpful for me:

https://www.researchgate.net/post/How_to_analyse_data_after_gromacs_simulation_of_protein