Why PAR is not RNA: ion atmospheres, bridging interactions, and ion-induced structural collapse

This folder contains the OpenMM code and input files used to generate Poly(ADP)-ribose (PAR) trajectories with the FIS-PAR model. The simulate.py is used to generate PAR trajectories. The code requires an input PDB file and a JSON configuration file. The provided file, input.json, specifies the parameters used to run the simulations. The data produced by this code is associated with the preprint “Why PAR is not RNA: ion atmospheres, bridging interactions, and ion-induced structural collapse” by Lipika Baidya, Peter Zhang, and Hung T. Nguyen (https://doi.org/10.1101/2025.11.29.691228).