Reimarging (wrapping)

In molecular modelling, the term “reimaging” (sometimes written “re-imaging” or “reimarging” in some texts) refers to the procedure of putting atoms or molecules back inside the primary simulation cell when periodic boundary conditions (PBCs) are used. 

In pDynamo3, when you run a molecular dynamics (MD) simulation with periodic boundary conditions (PBC), the system is simulated in a finite box that is periodically replicated in all directions. As atoms move, some may cross the box boundaries. By default, pDynamo3 does not automatically display them on the opposite side of the box (their periodic images). Therefore, reimaging is required to ensure that entire molecules are kept intact, not just individual atoms.

In EasyHybrid, you can access the reimaging tool as follows:

Open the Main Menu.

Go to Analysis.

Select Reimaging (wrapping).

In the Reimaging window, you must choose which system/coordinate set you want to correct. 

By geometric center: When the geometric center of a molecule crosses the boundary of the simulation box, the molecule is automatically repositioned on the opposite side.

Center the selection in the box: If this option is enabled, the algorithm first shifts the geometric center of the selected atoms to the center of the box, and then reorganizes (reimages) the remaining molecules accordingly.