From: Sourav Ray (
Date: Fri Apr 01 2016 - 16:28:45 CDT


I am trying to replicate the aggregation of four coarse-grained peptides.
Although during the course of simulation, I observe a trimer formation, but
after unwrapping, the trimer is no longer there. My questions are:

1. Is the unwrapped visualization correct or the wrapped one?
2. While calculating the inter-peptide distance, shall I follow the
minimum-image convention or calculate the distance from the unwrapped

I am using the pbc command below to unwrap the peptide molecules:

pbc unwrap -sel "segname P1 P2 P3 P4"

Thanks and regards