Hi everyone
   I want study the coagulation (aggregation) in the cell. I use two criterias to define the coagulation of two molecules:one is that  the distance between center of mass is smaller than a certain value; another on is that this situation should lasts for enough long time.I have 100 molecules in cell (periodical bondary condition),aand I want to calculate the distance between molecule pairs. But I have a problem, the molecules go out of the cell and some new molecules go into the cell during the simulation due to the PBC. That means two molecules will be in two seperated cells during the md simulation, but I just want to calculate the distance between molecules in the same cell.My script can not do it.
    My first question is how to monitor the distance between molecule pairs in the same cell? My second question is if I can not do that in MS, is there a better way to define the coagulation between molecules in MS?

The module I used is Forcite,and the version is MS 6.0.

Any help is appreciated.
Thanks a lot 
Sincerely 
Li