Dear all, In my simulation, when the simulation box shrinks, the center of box always shift towards the origin even if the center motion is set to removed every timestep. I just wonder if there is an anticipated center position for a given simulation box in gromacs. The box type is dodecahedron in my simulation.
My problem is how to make sure a group of atoms, such as proteins, sit at the center of the simulation box after the simulation box become stable. Current, as the center of the box floats, it is very difficult to maintain it by position restraint of the center group. Thank you in advance for any suggestions! with best wishes Zhenlong
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