I am a new graduate student trying to simulate a linear polymeric melt system using LAMMPS. I use the bead spring model, and the trial system is 100_chain_length * 100_chain_number, the density is 0.85 at T=1.0.
I used the bond/swap fix to relax the system for several million timesteps. I wanted to calculate the end-to-end distance of the chains to monitor how the configuration of the system was changing with time and that is where I encountered a problem. For a given chain, that was involved in bond swapping, while the unscaled atom coordinates look fine in the most part, the box images don’t make sense since generating actual positions of beads using those two information results in unrealistic bond distance between bonded beads. I think, since bond swapping is done based on neighbor list (that is using unscaled positions of the beads) I wonder if the box images of the beads are properly taken care of after bond swapping happens between two chains. Any advice on how to solve the problem I’m having is highly appreciated.