Tuesday, September 20, 2011

QM molecular dynamics

In classical molecular dynamics simulations, we follow the evolution of a system of particles that interact with each other according to newtonian mechanics. The correct description of chemical bonds, angles and torsions in classical mechanics can only be achieved by introducing carefully parameterized expressions that represent the change in electronic energy upon stretching/compressing a bond, or bending an angle. These parameterized force fields (AMBER, CHARMM, GROMOS, YASARA, OPLS) allow the simulation of very large systems (>10000 atoms) for long simulation times (>20 ns) with an obvious drawback: the quality of the simulations is only as good as the quality of the parameterized expressions, and therefore one is limited to the simulation of specific classes of previously characterized molecules/functional groups. Simulating chemical reactions is generally not possible without special protocols (like thermodynamic integration).

Ab initio molecular simulations (e.g. Car-Parrinello MD) are much more expensive, and are generally limited to (at most) a few dozen atoms and <100 ps. Two papers from Prof. Shogo Sakai's group show that QM molecular simulations can be performed with considerable time-savings if the system is partitioned into several smaller systems. They have not yet developed the theory to the point where one can attempt bond-breaking, but theirs seems a fruitful approach to the problem.

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