plotheights

hills

time in the first column of the HILLS file will be ignored.

ignoretime

a title for the x axis: see 'title'.

xlab

a title for the y axis: see 'title'.

ylab

numeric vector of length 2, giving the x coordinates range.

xlim

numeric vector of length 2, giving the y coordinates range.

ylim

an overall title for the plot: see 'title'.

main

a sub title for the plot: see 'title'.

the y/x aspect ratio, see 'plot.window'.

line width for drawing symbols see 'par'.

a logical value indicating whether both axes should be drawn
on the plot.

axes

`plotheights` plots evolution of heights of hills. In well tempered metadynamics
hill heights decrees with flooding of the free energy surface. Evolution of heights
may be useful to evaluate convergence of the simulation.

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.

plotheights: Plot evolution of heights of hills (generic function for 'metadynminer' and 'metadynminer3d')

Description

Usage

Arguments