2.1.3. Production Simulations

Unbiased canonical (NVT) ensemble MD was run using CHARMM software with the OpenMM GPU acceleration interface [87–92] on CUDA platform and GTX 1080 Ti graphics cards (NVIDIA Corp., Santa Clara, USA.). Non-bonded interaction truncations and energy calculations were performed using the same methods from the heating stage, and Ewald summation of Gaussian electrostatic charge density distributions [93,94] with a width of 0.320 was performed. The SHAKE algorithm [77] was used to constrain all water geometries and bonds involving hydrogen atoms using bond distances from the parameter table and the leapfrog Verlet integration algorithm [95] was used for Langevin dynamics

with a friction coefficient of 0.1 ps−<sup>1</sup> , a constant temperature of 310 K, and a 0.002-ps timestep. Prior to production, each of four replicates was equilibrated for 50,000 steps (100 ps). Simulations were run for 250,000,000 steps (500 ns) and atomic coordinates were saved at 25,000-step (50-ps) intervals for analyses (10,000 snapshots per quadruplicate simulation). ‐ ‐ ‐ ‐
