Question

Difference between molecular dynamics and energy minimization

Answer 1

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The difference between energy minimization and molecular dynamic simulation can be summarized like this. All molecules can exist with relative atom placements that are energetically unfavorable (i.e. it requires input of energy to put a molecule into a particular conformation). All molecules also have one (or more) optimal atom placements, where any change in any atom position will require input of energy. This is a minimum energy (ME) conformation. Energy minimization is the process of computationally finding the closest ME conformation. Because of the way minimization algorithms work, the located minimum may not actually be the global ME but instead a local minima. In other words, any slight atom movement away from the local ME conformation will require imput of energy, so it is indeed a minimum. However, there could be other quite different atomic arrangements that actually have a lower ME but energy minimization alone may not find these.

Molecular dynamics is the computational process of simulating molecular motion. Similar (or identical) "forcefields" are used as is the case with energy minimization algorithms. In this case, the goal is not to reduce energy to the closest ME conformation but to more or less conserve energy while allowing atoms to move about (while constrained by the forcefield). If allowed to proceed long enough, such dynamic simulations can often sample quite different molecular conformations, especially if the amount of starting energy is high (e.g. "high temperature"). Coupled with energy minimization, such dynamic simulation protocols (e.g. monte carlo) have a better chance of finding correct global ME conformations than simply starting with a (random?) conformation and minimizing that.... (You also can learn things about how the molecule moves and what conformations are likely populated most of the time)

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