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 …

Metadynamics is an atomistic simulation technique that allows, within the same framework,
acceleration of rare events and estimation of the free energy of complex molecular systems …

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 …

Despite tremendous successes in the field of antibiotic discovery seen in the previous
century, infectious diseases have remained a leading cause of death. More specifically …

Although molecular dynamics simulations have become a useful tool in essentially all fields
of chemistry, condensed matter physics, materials science, and biology, there is still a large …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Metadynamics is a popular enhanced sampling algorithm for computing the free energy
landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

Background Molecular dynamics has emerged as an important research methodology
covering systems to the level of millions of atoms. However, insufficient sampling often limits …

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 …