  The molecular simulations solve the equation of motion of molecular systems,
making 3D shapes of molecules four-dimensional by adding the time coordinate.
These methods have a great potential in drug discovery because they can
realistically model the structures of protein molecules targeted by drugs as
well as the process of binding of a potential drug to its molecular target.
However, routine application of biomolecular simulations is hampered by the
very high computational costs of this method. Several methods have been
developed to address this problem. One of them, metadynamics, disfavors states
of the simulated system that have been already visited and thus forces the
system to explore new and new states. Here we present the package metadynminer
and metadynminer3d to analyze and visualize results from metadynamics, in
particular those produced by a popular metadynamics package Plumed.
