Understanding the function of biological macromolecules and their complexes at the
physicochemical level requires knowledge of both their structure and dynamics …

Molecular dynamics simulations rely on integrating the classical (Newtonian) equations of
motion for a molecular system and thus, sample a microcanonical (constant-energy) …

Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …

We describe the development, current features, and some directions for future development
of the AMBER package of computer programs. This package has evolved from a program …

We present the newest version of the GROningen MOlecular Simulation program package,
GROMOS96. GROMOS96 has been developed for the dynamic modelling of (bio) molecules …

Nucleic acid molecules play a central role in cell biological processes. DNA's main role is to
act as the carrier of genetic information. Furthermore, DNA is transcribed into RNA by a …

Paramagnetic relaxation enhancement (PRE) measurements on 1H nuclei have the
potential to play an important role in NMR structure determination of macromolecules by …

Historically, experimental measurements have been used to bias biomolecular simulations
toward structures compatible with those observations via the addition of ad hoc restraint …

In order to characterise the dynamics of proteins, a well-established method is to incorporate
experimental parameters as replica-averaged structural restraints into molecular dynamics …

By employing thousands of PCs and new worldwide-distributed computing techniques, we
have simulated in atomistic detail the folding of a fast-folding 36-residue α-helical protein …