PBC issues when simulating multimeric assembly

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GROMACS version: 2025.2
GROMACS modification: Yes/No
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Hi,
We performed MD simulations of six monomers that progressively assemble into a hexamer. The raw trajectories were post-processed by first applying -pbc nojump and subsequently -pbc whole, selecting the six monomers as one selection during the -pbc whole step for trajectory fitting.

However, we observed that when oligomers approach the edges of the box, individual monomers appear on opposite sides of the periodic box, resulting in an apparent fragmentation of the oligomer. Since all six monomers were selected for fitting, we expected the nojump/whole procedure to preserve the integrity of the assembled oligomers.

Can you please advise on how to properly treat periodic boundary conditions in this case to ensure that oligomeric assemblies remain intact throughout the trajectory? We are performing markov state modeling and the oligomers are not recognized as such because in the frames they appear fragmented due to this PBC artifact.

Thanks!

2

You may need to play around with the PBC options to figure out which selection works as there’s no universal set of commands that works every time. Maybe try selecting a specific monomer or set of monomers to center as part of the commands