Hi everyone,

I'm performing Dissipative Particle Dynamics (DPD) simulations using the MesoDyn module in BIOVIA Materials Studio 2022 (version 22.1.1.11). My system consists of PNIPAM polymer chains grafted onto a silica substrate, with water as the solvent. I aim to study the temperature-dependent conformational changes of the polymer by calculating the radius of gyration of PNIPAM chains from trajectories obtained at different temperatures (278 K, 298 K, and 308 K).

However, when I attempt to calculate the radius of gyration, I encounter the following error:

"Radius of gyration analysis failed. There are no suitable particles for analysis that are not in infinite networks."

I suspect this is due to some polymer chains extending outside the primary simulation cell, thus causing the chains to appear as infinite due to periodic boundary conditions.

I've attempted a temporary solution by using:

• Display style → Lattice tab → setting Range (axis B) to 2, effectively visualizing an additional periodic image of the simulation cell.
• Then, selecting and moving the extended polymer segments back into the original cell.

However, I realized this approach only modifies a single snapshot rather than the entire trajectory, which is critical for calculating the radius of gyration accurately.

I also considered manually detaching and re-centering polymer chains, but this would disrupt the integrity of the recorded trajectories, thus making it unsuitable for my analysis.

Could anyone suggest an effective and proper way to resolve periodic boundary conditions issues in Materials Studio to calculate the radius of gyration accurately from the entire trajectory?

Any insights or alternative approaches would be greatly appreciated!

I've attached screenshots illustrating the issue and my software version for clarity.

Thanks very much for your help!