The barrier for heme–protein separation estimated by non-equilibrium molecular dynamics simulations

On multiscale non-equilibrium molecular dynamics simulations

In this work, we set forth a multiscale non-equilibrium molecular dynamics (MS-NEMD) model. The main objectives of MS-NEMD model are: (1) establishing a rigorous NEMD that provides direct threedimensional simulations of thermal–mechanical motions at atomistic scale, and (2) providing a general computational paradigm for non-equilibrium multiscale simulations. The proposed MS-NEMD combines a coa...

Non-equilibrium Molecular Dynamics

Statistical mechanics provides a well-established link between microscopic equilibrium states and thermodynamics. If one considers systems out of equilibrium, the link between microscopic dynamical properties and nonequilibrium macroscopic states is more difficult to establish [1,2]. For systems lying near equilibrium, linear response theory provides a route to derive linear macroscopic laws an...

Dynamical Non-Equilibrium Molecular Dynamics

In this review, we discuss the Dynamical approach to Non-Equilibrium Molecular Dynamics (D-NEMD), which extends stationary NEMD to time-dependent situations, be they responses or relaxations. Based on the original Onsager regression hypothesis, implemented in the nineteen-seventies by Ciccotti, Jacucci and MacDonald, the approach permits one to separate the problem of dynamical evolution from t...

Long Range Corrections to the Vapor-Liquid Equilibrium and Surface Tension of Methane with NVT Molecular Dynamics Simulations

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations

With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readil...