[gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

[Adarsh V. K.]

Dear all,

We have a 419 amino acid long protein and planned Protein-ligand complex MD
simulation using Gromacs 5.1.4 to check.

 1. What sought of MD simulation we have to perform?.
 2. Restrain protein alone or Restrain both protein and ligand during
simulation?.
 3. What is the exact command for Drug positional RMSD plot?
 4. What is the exact command for Number of Hydrogen bond plot?
 5. What is the exact command for Other interactions between protein and
ligand?
 6. how to view the trajectory files? or We have to convert the frames to
*.pdb and view in Pymol?

Regards,
Adarsh V. K.