metadynminer (version 0.1.7)

neb: 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

# NOT RUN {
tfes<-fes(acealanme, imax=5000)
minima<-fesminima(tfes)
nebAD<-neb(minima, min1="A", min2="D", nsteps=20)
nebAD
# }