fesminima

inputfes

<p>number of bins for each CV (default 8).</p>

nbins

<p>`fesminima` finds free energy minima on 1D or 2D free energy surface.
The surface is divided by a 1D or 2D grid and minima are found for each
bin. Next the program determines whether the minimum of a bin is a local
minimum of the whole free energy surface. Free energy minima are labeled
constitutively by capital letters.</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.

fesminima: Find free energy minima in the fes object (generic function for 'metadynminer' and 'metadynminer3d')

Description

Usage

Arguments

Value