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 …

Proteins are the molecular machinery of the human body, and their malfunctioning is often
responsible for diseases, making them crucial targets for drug discovery. The 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 …

Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …

Molecular dynamics simulations require barostats to be performed at a constant pressure.
The usual recipe is to employ the Berendsen barostat first, which displays a first-order …

Virtual high throughput screening (vHTS) in drug discovery is a powerful approach to identify
hits: when applied successfully, it can be much faster and cheaper than experimental high …

Free-energy calculations have seen increased usage in structure-based drug design.
Despite the rising interest, automation of the complex calculations and subsequent analysis …

The recent advances in relative protein–ligand binding free energy calculations have shown
the value of alchemical methods in drug discovery. Accurately assessing absolute binding …

The goal of the present manuscript is to succinctly trace the key technological steps in the
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …

The calculation of harmonic vibrational frequencies (HVF) to interpret infrared (IR) spectra
and to convert molecular energies to free energies is one of the essential steps in …