fespoint

hills

coordinates of the point in the CV space.

coord

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

imin

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

imax

if TRUE, the output is verbose (default TRUE).

verb

`fespoint` calculates free energy at given point in the CV space 'coord'.
Hills are summed from 'imin' to `imax`. Printed output can be suppressed by setting
'verb' to TRUE.

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.

fespoint: Calculate free energy at given point in the CV space (generic function for 'metadynminer' and 'metadynminer3d')

Description

Usage

Arguments