Well-Tempered MetaDynamics based method to evaluate universal peptidomimetics

Linking well-tempered metadynamics simulations with experiments.

Linking experiments with the atomistic resolution provided by molecular dynamics simulations can shed light on the structure and dynamics of protein-disordered states. The sampling limitations of classical molecular dynamics can be overcome using metadynamics, which is based on the introduction of a history-dependent bias on a small number of suitably chosen collective variables. Even if such b...

Well-tempered metadynamics: a smoothly converging and tunable free-energy method.

We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only ...

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster ...

The Well-tempered Computer

The psychological mechanism by which even musically untutored people can comprehend novel melodies resembles that by which they comprehend sentences of their native language. The paper identifies a syntax, a semantics, and a domain or “model”. These elements are examined in application to the task of harmonic comprehension and analysis of unaccompanied melody, and a computational theory is argu...

The Well-Tempered Critic