MacroModel Dynamics Calculations

Molecular dynamics simulations in MacroModel use classical mechanics (Newton’s equations of motion) to mimic how the system would behave as a function of time, typically at or close to the temperature of interest. You can use molecular dynamics studies to learn about the thermal variations within a system or to permit it to relax out of a local minimum structure into related but more probable structures.

You can use the Dynamics Panel to set up dynamics calculations and either submit the calculation or write the job files for later use.

It is often difficult to know when you have sampled enough in a molecular dynamics simulation. It usually is helpful to have some prior knowledge of the time-scales for crucial processes within the system to know if convergence may have been achieved.

While molecular dynamics simulations provide a wealth of structural and temporal information, the information is often hard to interpret. If the goal is to thermally sample the local conformational minimum of a small molecule, then you might not need to examine the results carefully provided that you have simulated sufficiently long (50 to 100 ps may be enough). However, if the system is large and the conformational variation is large, simulations likely will not adequately sample the conformations available, and careful, problem-specific consideration of the results may be needed to learn from such studies. In such circumstances, it almost always helps to examine the trajectory visually with a tool such as the ePlayer. In addition, clustering tools may help you identify when key events occurred during the simulation.