Md results

GROMACS version:2021
GROMACS modification: No

I’m new in Gromacs and molecular dynamics:

could you please help me with the code I have to write to get:

  • intermolecular hydrogen bonds interactions.
  • binding free energy and radius of gyration for the elucidation of conformational.
  • structural and compactness of the protein-liganed.


30ns is it enough for a complex protein-ligand? because I have read a comment from a researcher, where he had said that: 10ns in enough complex protein-ligand; and we have to reach 100-1000 ns for studying the stability of a protein structure alone.

thanks for you time.

These things requires you to have a good insight of MD first. I would recommend to start doing some tutorials and hand on here.

1 Like

thank you for your response.
I have followed the mentioned tutorials, and they have work for me very well, but i didn’t find the command lines.
I already did protein-ligand simulation tutorials in gromacs for my complex. and i want to analyze protein-ligand interactions, now i want to calculate the RMSD calculation of complex and hydrogen bond stabilization and radius of gyration.

1- For RMSD, i have chose :

  • backbone-protein_ligand for the complex
    -backbone-protein for the protein
    -backbone-ligand for the ligand (the results shown in the attached image)
    I’m correct? and based on the results my complex is not stable?

2- and for intermolecular hydrogen bonds interactions: I did not find the complex in the list so I have chose the protein then the ligand and i have got 0 H-bonds (but based on docking results, there are H-bonds with length 1.7A), Is it normal or I have made a mistake some where?

3- for binding free energy and structural and compactness of the protein-liganed. I could not find how to get the results CAN SEND YOU SOME USEFUL COMMANDS.

4- what are Umbrella sampling and PCA, and how to do them?

5- are those analyses enough for prot-ligand complex? please anyone can give me other suggestions?

thank you very much for your time.