Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …

The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel …

Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …

Scoring functions are a class of computational methods widely applied in structure-based
drug design for evaluating protein–ligand interactions. Dozens of scoring functions have …

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 …

In the following section, we will recapitulate selected experimental milestones through the
eyes of the theoretician, which, in our opinion, significantly advanced the field of covalent …

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

Plants counteract fluctuations in water supply by regulating all aquaporins in the cell plasma
membrane. Channel closure results either from the dephosphorylation of two conserved …

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