Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …

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 …

It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …

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 …

QM/MM simulations have become an indispensable tool in many chemical and biochemical
investigations. Considering the tremendous degree of success, including recognition by a …

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

Roughly half of the drug overdose-related deaths in the United States are related to
synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor …

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

Constant pH molecular dynamics (MD) simulations sample protonation states on the fly
according to the conformational environment and user specified pH conditions; however, the …

In bionanotechnology, the field of creating functional materials consisting of bio-inspired
molecules, the function and shape of a nanostructure only appear through the assembly of …