acealanme3d

<p>Hills from 30 ns metadynamics of AceAlaNme (Amber99SB-ILDN) in water (TIP3P)
with a Ramachandran dihedral phi and psi and peptide bond torsion omega as
the collective variable.</p>

datasets

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.
As an addendum, 'metadynaminer3d' is used to visualize 3D hills. 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. Free energy surfaces and minima can be plotted to produce
publication quality images.

Vojtech Spiwok

metadynminer3d

acealanme3d: Hills from 30 ns metadynamics of AceAlaNme in water with three collective variable

Description

Usage

Arguments

Format