[gmx-users] Self-interaction across periodic boundaries

[Salman Zarrini]

Dear all,
Using MD simulations I expect to observe aggregation among some molecules
solvated in water to have ultimately a droplet out of the molecules. The
aggregates form to some extent in the course of simulation time, however,
after a while the system become kinetically trapped in artificial
percolating aggregates in which the molecules are self-interacting across
the periodic boundaries.
I wonder if there is any possibility to prevent aggregates self-interaction
across periodic boundaries?

Thank you,
Salman
-- 
Best regards,

Salman Zarrini