# Topology and force-field parameters for Rhodamine B in water

**URL:** <https://gromacs.bioexcel.eu/t/topology-and-force-field-parameters-for-rhodamine-b-in-water/13657>\
**Category:** User discussions\
**Tags:** forcefield, simulation-setup\
**Created:** [August 10, 2026, 11:48pm UTC](https://gromacs.bioexcel.eu/t/topology-and-force-field-parameters-for-rhodamine-b-in-water/13657 "2026-08-10T23:48:10Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Chann](https://avatars.discourse-cdn.com/v4/letter/c/b487fb/32.png) [@Chann](https://gromacs.bioexcel.eu/u/Chann)\
**Post date:** [August 10, 2026, 11:48pm UTC](https://gromacs.bioexcel.eu/t/topology-and-force-field-parameters-for-rhodamine-b-in-water/13657/1 "2026-08-10T23:48:10Z")

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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.