(see the GitHub link to the OLIVES script below) using a cutoff of 0.55 nm for generating the secondary and tertiary networks. The LJ bond energies were unmodified values from Table as described in Figure . As an illustration of how to apply OLIVES in practice, the following command line prompt will convert the (prepared) atomistic protein complex of The Martini 3 simulations were carried out using GROMACS v2021.4 on Nvidia V100 GPUs at CSCAA. We used standard Martini 3 settings 1 with reaction field electrostatics (cutoff 1.1 nm, ϵ r = 15, ϵ rf = 0) and for Van der Waals interactions we used potentialshift-verlet with cutoff 1.1 nm. We used some important neighbor-list changes recently recommended by Kim et al. Specifically, we turned off the dual pair list by setting verletbuffer-tolerance = -1, set rlist = 1.35, and set nstlist = nsttcouple = nstpcouple = 20.