Hi all,
i am simulating phase separation of polymers in an implicit solvent (using LAMMPS (7 Feb 2024 - Update 1)). For the setup I have, I have confirmed that the polymer-rich and polymer-poor phases will form, i.e. there will be a roughly spherical droplet with some polymers floating around and exchanging with the ones in the droplet.
As expected, the droplet often appears “broken” due to PBCs and I would like to make the droplet “whole”. I have thought about:
a)
- storing unwrapped trajectory
- wrapping the whole polymers back to the primary unit cell. Here I could wrap the polymer based on the location of the center of mass, but this decision is rather arbitrary and does not guarantee that I will be able to reconstruct the droplet.
b) start with a fairly uniformly dispersed polymers and use fix recenter to keep the C.O.M. of the whole system at the center of the box.
I am not fully happy with any of the presented options. Has anyone else had a similar problem? I know that in Gromacs one can get around it by invoking a number of gmx trjconv commands, but overall LAMMPS is more suited for my needs.
I would be happy to hear your suggestions and experience.
Best,
Anze