Non-equilibrium molecular dynamics (NEMD) simulation has been recognized as a powerful
tool for examining biomolecules and provides fruitful insights into not only non-equilibrium …

Equilibrium molecular dynamics has been generalized to simulate nonequilibrium systems
by adding sources of thermodynamic heat and work. This generalization incorporates …

Some time ago, Ciccotti and Jacucci [Phys. Rev. Lett. 1975; 35: 789-792]–on the basis of
Onsager regression hypothesis as explained by Kubo–suggested and implemented an …

Calculation of free energy is of great importance for understanding the kinetics and the
structural determinants of biomolecular processes, such as transition between different …

Non-equilibrium molecular dynamics (NEMD) simulations provide a powerful tool to
investigate non-equilibrium phenomena from a microscopic perspective by taking into …

Steered molecular dynamics (SMD) permits efficient investigations of molecular processes
by focusing on selected degrees of freedom. We explain how one can, in the framework of …

As standard unbiased molecular dynamics (MD) simulations become impractical for
sampling rare events,“targeted MD” employs a moving distance constraint to enforce rare …

The computation of free energy differences through an exponential weighting of out-of-
equilibrium paths (known as the Jarzynski equality [C. Jarzynski, Equilibrium free energy …

The calculation of free energy profiles is central in understanding differential enzymatic
activity, for instance, involving chemical reactions that require QM‐MM tools, ligand …

Molecular dynamics (MD) simulations represent the computer approach to statistical
mechanics. As a counterpart to experiment, MD simulations are used to estimate equilibrium …