GROMACS modification: No
Hello all.I performed an MD simulation on a laccase containing 4 Cu ions in water solvent without any substrate.
simulation run without any error, but when i used vmd for visualizing the last trajectory, one of the ions that was complexed by His and cys, has changed its place and is not inside the protein at the end of simulation time. Is this simulation reliable or not? how can i keep cu fixed in protein during the MD simulation?
I used charmm-gui to generate input files for simulation.