Dear GMXers,
I’m trying to do a MD run with my protein in water but after EM-through steep and cg- the program runs a MD and give me after some steps a message: “atom 108708 can not be settled. Check for bad contacts and/or reduce the timestep”. I tried to do this but the problem persist.
I’m using LINCS for constraints my geometry at MD and EM gave a system with lower potential energy, e.g., -1 exp+6.Can anyone help me?
Thanks,
Samuel Pita.


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