In molecular dynamics (MD) simulations, the interactions between the particles of a system are described by classical potentials. For the many-particle system, Newton's equations of motion are solved per iteration. In this way, we obtain a deterministic trajectory of the system in phase space.

10,000 particles for a microsecond

Thus, MD simulations allow to obtain the complete microscopic information about the simulated system. This knowledge can be used to calculate observables by ensemble and time averaging. The time window of MD simulations is determined by computer power. Nowadays, assuming a computer time of one week, it is possible to follow the time evolution of a classical 10000 particle system for ca. 1 microsecond.

When striving for MD simulations of larger systems for longer times, it is useful to move from all-atom to coarse-grained descriptions. In such coarse-grained models, several atoms are grouped together to form a particle. While this approach allows one to strongly reduce the number of pair interactions to be calculated, it remains an active field of research to derive coarse-grained interaction potentials from the underlying all-atom force fields in a systematic manner. We tackle this problem in the framework of a DFG collaborative research center (TRR 146).

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