Package: metadynminer 0.1.7

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

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.

Authors:Vojtech Spiwok [aut, cre]

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metadynminer.pdf |metadynminer.html
metadynminer/json (API)

# Install 'metadynminer' in R:
install.packages('metadynminer', repos = c('https://spiwokv.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/spiwokv/metadynminer/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • 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

On CRAN:

5.35 score 31 stars 1 packages 48 scripts 206 downloads 15 exports 1 dependencies

Last updated 11 months agofrom:026be749a7. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64OKOct 31 2024
R-4.5-linux-x86_64OKOct 31 2024
R-4.4-win-x86_64OKOct 31 2024
R-4.4-mac-x86_64OKOct 31 2024
R-4.4-mac-aarch64OKOct 31 2024
R-4.3-win-x86_64OKOct 31 2024
R-4.3-mac-x86_64OKOct 31 2024
R-4.3-mac-aarch64OKOct 31 2024

Exports:emptyhillsfeproffesfes2fes2d21dfesminimafespointlinesonfesneboneminimumplotheightspointsonfesprobread.hillsread.plumed

Dependencies:Rcpp

Readme and manuals

Help Manual

Help pageTopics
Hills from 30 ns metadynamics of AceAlaNme in water with two collective variablesacealanme
Hills from 30 ns metadynamics of AceAlaNme in water with one collective variableacealanme1d
Generate empty HILLS from Plumedemptyhills
Calculate free energy profile for minima object (generic function for 'metadynminer' and 'metadynminer3d')feprof
Calculate free energy profile for minima objectfeprof.minima
Calculate free energy surface by Bias Sum algorithm (generic function for 'metadynminer' and 'metadynminer3d')fes
Calculate free energy surface by Bias Sum algorithmfes.hillsfile
Calculate free energy surface by conventional algorithm (generic function for 'metadynminer' and 'metadynminer3d')fes2
Calculate free energy surface by conventional algorithmfes2.hillsfile
Calculate 1D free energy surface from hillsfile objectfes2d21d
Find free energy minima in the fes object (generic function for 'metadynminer' and 'metadynminer3d')fesminima
Find free energy minima in the fes objectfesminima.fes
Calculate free energy at given point in the CV space (generic function for 'metadynminer' and 'metadynminer3d')fespoint
Calculate free energy at given point in the CV spacefespoint.hillsfile
Print first n lines of hillsfilehead.hillsfile
Plots 1D free energy surface object as lineslines.fes
Plot lines for hillsfile objectlines.hillsfile
Plot lines for Nudged Elastic Bandlines.nebpath
Plot lines for Nudged Elastic Band projected onto free energy surfacelinesonfes
Calculate maximum of free energy surfacemax.fes
Calculate minimum of free energy surfacemin.fes
Find transition path on free energy surface by Nudged Elastic Band methodneb
Creates one ad hoc free energy minimum for a fes object (generic function for 'metadynminer' and 'metadynminer3d')oneminimum
Creates one ad hoc free energy minimum for a fes objectoneminimum.fes
Plot free energy surface objectplot.fes
Plot hillsfile objectplot.hillsfile
Plot minima objectplot.minima
Plot Nudged Elastic Bandplot.nebpath
Plot free energy profileplot.profiles
Plot evolution of heights of hills (generic function for 'metadynminer' and 'metadynminer3d')plotheights
Plot evolution of heights of hills in hillsfile objectplotheights.hillsfile
Plots 1D free energy surface object as pointspoints.fes
Plot points for hillsfile objectpoints.hillsfile
Plot points for Nudged Elastic Bandpoints.nebpath
Plot points for Nudged Elastic Band projected onto free energy surfacepointsonfes
Print dimensionality, minimum and maximum of free energy surfaceprint.fes
Print hillsfileprint.hillsfile
Print minima objectprint.minima
Print Nudged Elastic Band minimaprint.nebpath
Print profiles objectprint.profiles
Calculate probability of free energy surfaceprob
Read HILLS from Plumedread.hills
Read 1D or 2D free energy surface from PLUMED sum_hillsread.plumed
Print summary of free energy surfacesummary.fes
Print summary for hillsfilesummary.hillsfile
Print minima object summarysummary.minima
Print summary for Nudged Elastic Bandsummary.nebpath
Print summary for free energy profilesummary.profiles
Print last n lines of hillsfiletail.hillsfile