fes2d21d {metadynminer}

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)