Computer simulation of molecular systems enables structure–energy–function relationships
of molecular processes to be described at the sub‐atomic, atomic, supra‐atomic, or supra …

Molecular dynamics (MD) simulations have become popular in materials science,
biochemistry, biophysics and several other fields. Improvements in computational resources …

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 …

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 …

We review a selection of methods for performing enhanced sampling in molecular dynamics
simulations. We consider methods based on collective variable biasing and on tempering …

Temperature control algorithms in molecular dynamics (MD) simulations are necessary to
study isothermal systems. However, these thermostatting algorithms alter the velocities of …

The flying ice cube effect is a molecular dynamics simulation artifact in which the use of
velocity rescaling thermostats sometimes causes violation of the equipartition theorem …

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of
nucleic acids. We explain physical chemistry limitations of the simulations, namely, the …

Previous work by us showed that in replica exchange molecular dynamics, exchanges
should be attempted extremely often, providing gains in efficiency and no undesired effects …

We investigate systematically the impacts of heat bath used in molecular dynamics
simulations on heat conduction in nanostructures exemplified by silicon nanowires (SiNWs) …