By Default the Simulation Protocols that use molecular dynamics reimage solute when the center of mass crosses one of the periodic box boundaries. This means the solute is translated to the opposite side of the box. This has no effect on the energetics, but if per-frame RMSDs are of central interest the behavior is not desirable. Usually the best option is to simply re-run using a more generous solvent layer, but if that is not acceptable for some reason the reimaging behavior can be turned off. The attached script is a modified version of the "Dynamics (Production)" protocol in which residue based reimaging of water and ions (salt) remains on, but all reimaging of solute is turned off.