GROMACS modification: Yes/No
Dear Gromacs users,
I am experiencing a problem, which is when I run a simulation with 1 MPI rank, I have a harmonic potential term added in the energy calculation. However, when I try to run the same simulation with more than 1 MPI rank, I lost that harmonic potential term. This caused my ligand to not stay in the binding site of my protein even though I already applied some distance restrains on the ligand and some key residues. I would really appreciated if any one could help me with this.
Here is the link to google drive that contain md.log and .mdp: