feprof

minims

<p>index of a hill from which summation stops (default the rest of hills).</p>

imax

<p>`feprof` calculates free energy profiles for free energy minima. It finds the global minimum
at the `imax` and calculates the evolution of free energies of a local vs. the global free energy
minimum. The free energy of the global minimum is constant (zero).</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.

feprof: Calculate free energy profile for minima object (generic function for 'metadynminer' and 'metadynminer3d')

Description

Usage

Arguments