The discussion revolves around the differences between the computational methods QM/MM (Quantum Mechanics/Molecular Mechanics) and QM/MD (Quantum Mechanics/Molecular Dynamics). Participants explore the theoretical underpinnings and applications of these methods in computational chemistry.
Participants do not reach a consensus on the specifics of the differences between QM/MM and QM/MD, and multiple competing views regarding their applications and implications remain present.
The discussion does not resolve the assumptions regarding the convergence behaviors of QM/MM and QM/MD, nor does it clarify the specific conditions under which each method is most applicable.
Programs like those in AMBER are used not only for calculating geometries and energies, but also for simulating molecular motion, i.e. for molecular dynamics, and for calculating the relative populations of various conformations or other geometric arrrangements (e.g. solvent molecule distribution around a macromolecule in Monte Carlo simulations. In molecular dynamics Newton's laws of motion are applied to molecules moving in a MM forcefield, although relatively small parts of the system (system: with biological molecules in particular modelling is often done not on an isolated molecule but on a molecule and its environment of solvent and ions) may be simulated with quantum mechanical methods. In Monte Carlo methods random numbers decide how atoms or molecules are moved to generate new conformations or geometric arrangements (states) which are then accepted or rejected according to some filter. Tens of thousands (or more) of states are generated, and the energy of each is calculated by MM, generating a Boltzmann distrubution.