neb: Find transition path on free energy surface by Nudged Elastic...

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

Find transition path on free energy surface by Nudged Elastic Band method

Description

'neb' finds a transition path on free energy surface for a given pair of minima. For a 1D surface it simply takes the free energy profile between the two minima. For 2D surface it calculates the transition path by Nudged Elastic

Usage

neb(minims = minims, min1 = "A", min2 = "B", nbins = 20,
  nsteps = 100, step = 1, k = 0.2)

Arguments

minims	minima object.
min1	starting minimum identifier (can be letter or index, default "A").
min2	final minimum identifier (can be letter or index, default "B").
nbins	number of bins along Nudged Elastic Band (default 20).
nsteps	number of Nudged Elastic Band iterations (default 100).
step	Nudged Elastic Band iteration step (default 1).
k	Nudged Elastic Band toughness (default 0.2).

Value

NEB path

Examples

tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
nebAD

metadynminer documentation built on April 14, 2022, 5:06 p.m.