Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files from 'Plumed'

[Up] [Top]

Documentation for package ‘metadynminer3d’ version 0.0.2

Help Pages

acealanme3d Hills from 30 ns metadynamics of AceAlaNme in water with three collective variable
feprof.minima3d Calculate free energy profile for minima3d object
fes.hillsfile3d Calculate 3D free energy surface by Bias Sum algorithm
fes2.hillsfile3d Calculate 3D free energy surface by conventional algorithm
fesminima.fes3d Find free energy minima in the fes3d object
fespoint.hillsfile3d Calculate free energy at given point in the CV space
head.hillsfile3d Print first n lines of hillsfile3d
max.fes3d Calculate maximum of 3D free energy surface
min.fes3d Calculate minimum of 3D free energy surface
oneminimum.fes3d Creates one ad hoc 3D free energy minimum for a fes object
plot.fes3d Plot 3D free energy surface object
plot.hillsfile3d Plot hillsfile3d object
plot.minima3d Plot minima3d object
plotheights.hillsfile3d Plot evolution of heights of hills in hillsfile3d object
print.fes3d Print minimum and maximum of 3D free energy surface
print.hillsfile3d Print hillsfile3d
print.minima3d Print minima3d object
read.hills3d Read 3D HILLS from Plumed
read.plumed3d Read 3D free energy surface from PLUMED sum_hills
summary.fes3d Print summary of 3D free energy surface
summary.hillsfile3d Print summary for hillsfile3d
summary.minima3d Print minima3d object summary
tail.hillsfile3d Print last n lines of hillsfile3d