I am doing a simulation of multiple polymers which are named with segnames U(integer). During the course of simulation two polymers U5 and U10 interact with each other. However, because of periodic boundary conditions when I measure the accessible area or radius of gyration I get unnaturally large values.
I have tried to wrap periodic boundaries by running the command
pbc wrap -all -centersel "segname U5 U10"
My reasoning is I want the U5 U10 aggregate at the center of the simulation box. However, this causes the polymer to fragment and again does not give proper result. Can you suggest proper pbc wrap arguments for this situtation?