fes2d21d: Calculate 1D free energy surface from hillsfile object

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

Calculate 1D free energy surface from hillsfile object

Description

'fes2d21d' calculates 2D free energy surface, converts free energies to probabilities (exp(-F/kT)), sums them up along one collective variable and converts back to free energy (-kT log(P)).

Usage

fes2d21d(hills, remdim = 2, temp = 300, eunit = "kJ/mol", imin = 1,
  imax = NULL, xlim = NULL, ylim = NULL, npoints = 256)

Arguments

hills	hillsfile object.
remdim	dimension to be removed (1 for CV1, 2 for CV2, default 2).
temp	temperature in Kelvins (default 300).
eunit	energy units (kJ/mol or kcal/mol, kJ/mol is default).
imin	index of a hill from which summation starts (default 1).
imax	index of a hill from which summation stops (default the rest of hills).
xlim	numeric vector of length 2, giving the CV1 coordinates range.
ylim	numeric vector of length 2, giving the CV2 coordinates range.
npoints	resolution of the free energy surface in number of points.

Value

fes object.

Examples

tfes<-fes2d21d(acealanme, remdim=2, imax=5000)

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