This seminar examined molecular-dynamics simulations of ureic compounds with attention to hydrogen-bond networks, solvent mediation, and conformational preferences under varying thermodynamic conditions. Presenters compared classical force-field parameterizations with ab initio-derived references, discussing trade-offs between sampling length and per-step accuracy. Emphasis was placed on thermostat/barostat choices and their influence on dynamical observables, as well as on diagnosing inadequate sampling via block-averaging and overlap metrics.
The discussion highlighted workflows that combine short ab initio trajectories for reference statistics with longer classical trajectories for population estimates. Practical guidance covered setup of protonation states, time-step selection relative to fastest modes, and solvent model implications for hydrogen-bond lifetimes. The session concluded with a compact checklist for reporting: ensemble definitions, equilibration criteria, restraint protocols, and uncertainty estimates that reflect both finite sampling and model error.