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

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Documentation for package ‘metadynminer’ version 0.1.7

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