[gmx-users] [gmx-user] MD simulation of protein-ligand complex

[Quin K]

Hi
Which of the following is the correct method to prepare a protein for
docking and then for protein-ligand complex MD simulation?

1. Do an MD simulation of protein for 100 ns and use the structure of
protein at 100 ns to do the protein-ligand MD simulation.
2. Do an energy minimization of protein (like 5 ns) and use that structure
for MD simulation of protein-ligand complex.

Kindly let me know

Thanks