Reconstructing a "broken droplet under PBCs"

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:


  1. storing unwrapped trajectory
  2. 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.


You could dump xtc, reverse-engineer suitable GROMACS topology and .gro files, and then use the GROMACS analysis tools on your XTC trajectory (as well as tools like MDAnalysis).

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Thanks for the suggestion.