free.energy: Free Energy from Molecular Dynamics Distributions
In s-cosseddu/RMD: General function to analyse MD simulations

Description Usage Arguments Details Examples

View source: R/free.energy.R

Given the distribution x of a degree of freedom of interest, the function computes the free energy at kT, according to

1	free.energy(x, kT = 0.616, zero.min = T, norm = T)

`x`	normalised or unnormalised distribution of the given degree of freedom
`kT`	(default 0.616)
`zero.min`	set the zero at the minimum of the free energy (default T)
`norm`	for debug normalisation of x can be disabled (default T)

F(x) = -kT*ln( pdf(x) ) + C

infile <- "test.data"
window.ll <- 20

x <- read.table(infile)
x <- ma(x, window.ll)
write.table(x,file=paste("ma",infile,sep="_"), quote=F, row.names=F, col.names=F)