Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files from 'Plumed'
Calculate free energy profile for minima3d object
Calculate 3D free energy surface by Bias Sum algorithm
Calculate 3D free energy surface by conventional algorithm
Find free energy minima in the fes3d object
Calculate free energy at given point in the CV space
Print first n lines of hillsfile3d
Calculate maximum of 3D free energy surface
Calculate minimum of 3D free energy surface
Creates one ad hoc 3D free energy minimum for a fes object
Plot 3D free energy surface object
Plot hillsfile3d object
Plot minima3d object
Plot evolution of heights of hills in hillsfile3d object
Print minimum and maximum of 3D free energy surface
Print hillsfile3d
Print minima3d object
Read 3D HILLS from Plumed
Read 3D free energy surface from PLUMED sum_hills
Print summary of 3D free energy surface
Print summary for hillsfile3d
Print minima3d object summary
Print last n lines of hillsfile3d
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.