Molecular simulation methods, such as molecular docking, molecular dynamic (MD)
simulation, and quantum chemical (QC) calculation, have become popular as …

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 …

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 …

Anton 3 is the newest member in a family of supercomputers specially designed for atomic-
level simulation of molecules relevant to biology (eg, DNA, proteins, and drug molecules) …

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC
resources to explore the time-dependent dynamics of molecular systems. We use this …

Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics
simulations that achieves significant gains in performance, programmability, and capacity …

The recent availability of long equilibrium simulations of protein folding in atomistic detail for
more than 10 proteins allows us to identify the key interactions driving folding. We find that …

OpenMM is a software toolkit for performing molecular simulations on a range of high
performance computing architectures. It is based on a layered architecture: the lower layers …

Molecular dynamics modeling has provided a powerful tool for simulating and
understanding diverse systems–ranging from materials processes to biophysical …

Biomacromolecules, including proteins and their complexes, adopt multiple conformations
that are linked to their biological functions. Though some of the structural heterogeneity can …