Function reference • metadynminer

All functions
`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

Reference

All functions