Advances over the past few years have begun to enable prediction and design of
macromolecular structures at near-atomic accuracy. Progress has stemmed from the …

Computation based on molecular models is playing an increasingly important role in
biology, biological chemistry, and biophysics. Since only a very limited number of properties …

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force
field is required. The Amber ff99SB force field improved protein secondary structure balance …

New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are
introduced. These parameter sets summarise some previously published force field …

Recent advances in hardware and software have enabled increasingly long molecular
dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of …

The development of reliable and extensible molecular mechanics (MM) force fields—fast,
empirical models characterizing the potential energy surface of molecular systems—is …

The stability of proteins in aqueous solution is routinely enhanced by cosolvents such as
glycerol. Glycerol is known to shift the native protein ensemble to more compact states …

We develop a detailed description of protein translational and rotational diffusion in
concentrated solution on the basis of all-atom molecular dynamics simulations in explicit …

The quality of biomolecular dynamics simulations relies critically on the force field that is
used to describe the interactions between particles in the system. Force fields, which are …

Protein folding and unfolding are coupled to a range of biological phenomena, from the
regulation of cellular activity to the onset of neurodegenerative diseases. Defining the nature …