Dear gromacs users, I am attempting to simulate a protein with an active site containing to metals (Ni and Fe). I am trying to mantain the active site structure constraining bonds, angles and dihedrals. When I simulate the active site alone in water, it remains stable. When I insert the active site in the protein's scaffold, unfortunately, the simulation crashes because of large vibration in bond lenght and angle amplitude in the active site. I am not able to detect big clashes or any structural distortion.
I tried to play with force constants, temperature, time-step, constrains, etc.etc. but I am not able to mantain the simulation stability. I am wondering whether exists a tool to dissect the energetic contributions ( including bonded parameters ) permitting me to identify the problem giving rise the crash. Francesco
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