This Review illustrates the evaluation of permeability of lipid membranes from molecular
dynamics (MD) simulation primarily using water and oxygen as examples. Membrane …

Highlights•Currently, developing a market-approved drug costs a staggering $2.6 billion.•In
silico methods have become an important strategy for narrowing down on promising lead …

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 …

Molecular dynamics (MD) computer simulations are used routinely to compute atomistic
trajectories of complex systems. Systems are simulated in various ensembles, depending on …

An increasingly important endeavor is to develop computational strategies that enable
molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in …

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Many important protein functions are carried out through proton-coupled conformational
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …

Development of a pH stat to properly control solution pH in biomolecular simulations has
been a long-standing goal in the community. Toward this goal recent years have witnessed …

Methods for the calculation of the p K a ionizable amino acids are valuable tools for
understanding pH-dependent properties of proteins. Cysteine is unique among the amino …

Predicting from first-principles the rate of passive permeation of small molecules across the
biological membrane represents a promising strategy for screening lead compounds …