Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'
Generate empty HILLS from Plumed
Calculate free energy profile for minima object
Calculate free energy profile for minima object (generic function for ...
Calculate free energy surface by Bias Sum algorithm
Calculate free energy surface by Bias Sum algorithm (generic function ...
Calculate free energy surface by conventional algorithm
Calculate free energy surface by conventional algorithm (generic funct...
Calculate 1D free energy surface from hillsfile object
Find free energy minima in the fes object
Find free energy minima in the fes object (generic function for 'metad...
Calculate free energy at given point in the CV space
Calculate free energy at given point in the CV space (generic function...
Print first n lines of hillsfile
Plots 1D free energy surface object as lines
Plot lines for hillsfile object
Plot lines for Nudged Elastic Band
Plot lines for Nudged Elastic Band projected onto free energy surface
Calculate maximum of free energy surface
Calculate minimum of free energy surface
Find transition path on free energy surface by Nudged Elastic Band met...
Creates one ad hoc free energy minimum for a fes object
Creates one ad hoc free energy minimum for a fes object (generic funct...
Plot free energy surface object
Plot hillsfile object
Plot minima object
Plot Nudged Elastic Band
Plot free energy profile
Plot evolution of heights of hills in hillsfile object
Plot evolution of heights of hills (generic function for 'metadynminer...
Plots 1D free energy surface object as points
Plot points for hillsfile object
Plot points for Nudged Elastic Band
Plot points for Nudged Elastic Band projected onto free energy surface
Print dimensionality, minimum and maximum of free energy surface
Print hillsfile
Print minima object
Print Nudged Elastic Band minima
Print profiles object
Calculate probability of free energy surface
Read HILLS from Plumed
Read 1D or 2D free energy surface from PLUMED sum_hills
Print summary of free energy surface
Print summary for hillsfile
Print minima object summary
Print summary for Nudged Elastic Band
Print summary for free energy profile
Print last n lines of hillsfile
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. 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. Transition states can be analyzed by Nudged Elastic Band method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy surfaces, minima and transition paths can be plotted to produce publication quality images.