Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

A software framework is introduced that facilitates the application of biasing algorithms to
collective variables of the type commonly employed to drive massively parallel molecular …

Hybrid methods that combine quantum mechanics (QM) and molecular mechanics (MM) can
be applied to studies of reaction mechanisms in locations ranging from active sites of small …

Markov state models (MSMs) based on molecular dynamics (MD) simulations are routinely
employed to study protein folding, however, their application to functional conformational …

Unregulated activation of Src kinases leads to aberrant signalling, uncontrolled growth and
differentiation of cancerous cells. Reaching a complete mechanistic understanding of large …

Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

An increasing number of studies have reported computations of the standard (absolute)
binding free energy of small ligands to proteins using molecular dynamics (MD) simulations …

Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …