Hello,

I know that this subject has sufficed several times but am not sure if the answers resolve my issue. I have a polymer chain of 15 monomers in a water box. The system is constructed using amorphous cell module. The chain just appears at the edge of the box and part of it outside. Changing the display style to in cell shows fragments of the polymer. If I must observe the interaction of the polymer with other molecules, am not sure how to interpret it if its fragmented. Would I bias results if I restrained the polymer to the center of the box and removed restraints in the production run? or is this behavior of leaving the cell unique to certain molecules and should be left that way for more meaningful simulations?