GROMACS version: 2023.3
GROMACS modification: Yes
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I am currently trying to simulate the protein ligand complex for 1 microsecond. I already did 1 ms simulation for 2 complex’s it was good and now I am trying to simulate my third complex but the issue is after 50, 150 or 200 nanosecond my RMSD goes all up to 6 nm or 5 nm and when I visualise the trajectory using VMD or Pymol the ligand was located in some other region as its automatically unbound from the protein.
what might be the reason for this kind of crazy RMSD and ligand unbound action ?
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