metadynminer3d

Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) doi:10.1016/j.cpc.2013.09.018 program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. As an addendum, 'metadynaminer3d' is used to visualize 3D hills. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) doi:10.1016/j.cpc.2015.08.037 to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Free energy surfaces and minima can be plotted to produce publication quality images.

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