This example can be found in the directory examples/sdamm_nambox.

In this example case, the geometry type is set to "nambox" to run the protein-ligand association at the presence of macromolecular crowders simulated using the adaptive model. Specifically, this example simualted the interaction between trypsing and benzamidine in the presence of charged lysozyme (HEW) at a concentration og 10 g/L. This example folder includes:

1. grid_prep: Contains the scripts and input files required to generate interaction grids for trypsin, benzamidine, and HEWL.
2. assoc: Contains the SDA input files needed to run the association simulation.

After running the simualtions the resulting trajectories can be analysed to explore binding pathways, using Markov State Modeling (MSM). More informations and instructions are written in the README.md present in the folder. Note: The following code has been tested on a HITS workstation, assuming APBS is available and accessible from the system environment. All simulation input files are configured to run on computing clusters accessible from HITS, using SLURM for job submission via sbatch.

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