Topology and force-field parameters for Rhodamine B in water

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GROMACS version: 2025.3
GROMACS modification: No

Hello everyone,

I am preparing an all-atom MD simulation of a single Rhodamine B molecule in explicit water. My goal is to calculate its translational diffusion coefficient from the MSD.

I found the work of Magalhães et al. (2022), “Interactions between Rhodamine Dyes and Model Membrane Systems—Insights from Molecular Dynamics Simulations.” They used GROMOS96 54a7/SPC and generated the Rhodamine parameters using ATB together with DFT calculations.

The paper states that Rhodamine coordinate and topology files were provided as supplementary material. However, the supplementary archive I can access contains only the supplemental figures.

Before parameterizing Rhodamine B myself, I would like to ask:

  1. Is there a published or well-validated GROMACS topology/parameter set for Rhodamine B (cationic or zwitterionic form)?
  2. Has anyone used or reproduced the topology from Magalhães et al.?
  3. If I need to build it myself, would you recommend reproducing the ATB/GROMOS54a7 workflow, or using a GAFF/GAFF2-based parameterization for diffusion in water?

Any references, topology files, or parameterization recommendations would be greatly appreciated.

Thank you.