Man pages for metadynminer
Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'
| acealanme | Hills from 30 ns metadynamics of AceAlaNme in water with two... |
| acealanme1d | Hills from 30 ns metadynamics of AceAlaNme in water with one... |
| emptyhills | Generate empty HILLS from Plumed |
| feprof | Calculate free energy profile for minima object (generic... |
| feprof.minima | Calculate free energy profile for minima object |
| fes | Calculate free energy surface by Bias Sum algorithm (generic... |
| fes2 | Calculate free energy surface by conventional algorithm... |
| fes2d21d | Calculate 1D free energy surface from hillsfile object |
| fes2.hillsfile | Calculate free energy surface by conventional algorithm |
| fes.hillsfile | Calculate free energy surface by Bias Sum algorithm |
| fesminima | Find free energy minima in the fes object (generic function... |
| fesminima.fes | Find free energy minima in the fes object |
| fespoint | Calculate free energy at given point in the CV space (generic... |
| 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... |
| 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... |
| oneminimum | Creates one ad hoc free energy minimum for a fes object... |
| oneminimum.fes | Creates one ad hoc free energy minimum for a fes object |
| plot.fes | Plot free energy surface object |
| plotheights | Plot evolution of heights of hills (generic function for... |
| plotheights.hillsfile | Plot evolution of heights of hills in hillsfile object |
| plot.hillsfile | Plot hillsfile object |
| plot.minima | Plot minima object |
| plot.nebpath | Plot Nudged Elastic Band |
| plot.profiles | Plot free energy profile |
| 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... |
| print.fes | Print dimensionality, minimum and maximum of free energy... |
| 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 |
