# Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'

## Documentation for package ‘metadynminer’ version 0.1.7

- DESCRIPTION file
- Package README

## Help Pages

acealanme | Hills from 30 ns metadynamics of AceAlaNme in water with two collective variables
acealanme1d | Hills from 30 ns metadynamics of AceAlaNme in water with one collective variable
emptyhills | Generate empty HILLS from Plumed
feprof | Calculate free energy profile for minima object (generic function for 'metadynminer' and 'metadynminer3d')
feprof.minima | Calculate free energy profile for minima object
fes | Calculate free energy surface by Bias Sum algorithm (generic function for 'metadynminer' and 'metadynminer3d')
fes.hillsfile | Calculate free energy surface by Bias Sum algorithm
fes2 | Calculate free energy surface by conventional algorithm (generic function for 'metadynminer' and 'metadynminer3d')
fes2.hillsfile | Calculate free energy surface by conventional algorithm
fes2d21d | Calculate 1D free energy surface from hillsfile object
fesminima | Find free energy minima in the fes object (generic function for 'metadynminer' and 'metadynminer3d')
fesminima.fes | Find free energy minima in the fes object
fespoint | Calculate free energy at given point in the CV space (generic function for 'metadynminer' and 'metadynminer3d')
fespoint.hillsfile | Calculate free energy at given point in the CV space
head.hillsfile | Print first n lines of hillsfile
lines.fes | Plots 1D free energy surface object as lines
lines.hillsfile | Plot lines for hillsfile object
lines.nebpath | Plot lines for Nudged Elastic Band
linesonfes | Plot lines for Nudged Elastic Band projected onto free energy surface
max.fes | Calculate maximum of free energy surface
min.fes | Calculate minimum of free energy surface
neb | Find transition path on free energy surface by Nudged Elastic Band method
oneminimum | Creates one ad hoc free energy minimum for a fes object (generic function for 'metadynminer' and 'metadynminer3d')
oneminimum.fes | Creates one ad hoc free energy minimum for a fes object
plot.fes | Plot free energy surface object
plot.hillsfile | Plot hillsfile object
plot.minima | Plot minima object
plot.nebpath | Plot Nudged Elastic Band
plot.profiles | Plot free energy profile
plotheights | Plot evolution of heights of hills (generic function for 'metadynminer' and 'metadynminer3d')
plotheights.hillsfile | Plot evolution of heights of hills in hillsfile object
points.fes | Plots 1D free energy surface object as points
points.hillsfile | Plot points for hillsfile object
points.nebpath | Plot points for Nudged Elastic Band
pointsonfes | Plot points for Nudged Elastic Band projected onto free energy surface
print.fes | Print dimensionality, minimum and maximum of free energy surface
print.hillsfile | Print hillsfile
print.minima | Print minima object
print.nebpath | Print Nudged Elastic Band minima
print.profiles | Print profiles object
prob | Calculate probability of free energy surface
read.hills | Read HILLS from Plumed
read.plumed | Read 1D or 2D free energy surface from PLUMED sum_hills
summary.fes | Print summary of free energy surface
summary.hillsfile | Print summary for hillsfile
summary.minima | Print minima object summary
summary.nebpath | Print summary for Nudged Elastic Band
summary.profiles | Print summary for free energy profile
tail.hillsfile | Print last n lines of hillsfile