fes2d21d

hills

dimension to be removed (1 for CV1, 2 for CV2, default 2).

remdim

temperature in Kelvins (default 300).

temp

energy units (kJ/mol or kcal/mol, kJ/mol is default).

eunit

index of a hill from which summation starts (default 1).

imin

index of a hill from which summation stops (default the rest of hills).

imax

numeric vector of length 2, giving the CV1 coordinates range.

xlim

numeric vector of length 2, giving the CV2 coordinates range.

ylim

resolution of the free energy surface in number of points.

npoints

`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)).

Metadynamics is a state of the art biomolecular simulation technique.
'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes
it possible to perform metadynamics using various simulation codes. The results of
metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package
'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package.
It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037>
to calculate a free energy surface from hills. Minima can be located and plotted on
the free energy surface. Transition states can be analyzed by Nudged Elastic Band
method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy
surfaces, minima and transition paths can be plotted to produce publication quality
images.

fes2d21d: Calculate 1D free energy surface from hillsfile object

Description

Usage

Arguments

Value

Examples