Part 7: Building the Molecular Dynamics Simulations

Relaxing the rigid-receptor approximation: force fields, matching two atom-naming schemes by graph isomorphism, solvating the box, staged equilibration, and the correction needed before measuring anything. Chapters 0:00 Title 0:06 Why simulate 0:35 Describing the parts 1:22 Matching the atom names 2:14 Building the box 2:57 Easing in 3:41 Nine trajectories 4:22 A correction that matters 5:11 How things were measured 5:56 Next Source Antor, S. A., Soash, M. A. S., Al Mahmud, M., Niloy, R. K., et al. (2026). Docking and molecular dynamics of the natural diterpenoid dihydrotanshinone I in human 15-PGDH across three inhibitor-bound receptor structures [Preprint]. Research Square. https://doi.org/10.21203/rs.3.rs-1071...