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 …

Like temperature and pressure, the solution pH is an important thermodynamic variable that
is commonly varied in experiments and is used by cells to influence biochemical function. It …

NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel …

We present the latest version of the Groningen Molecular Simulation program package,
GROMOS05. It has been developed for the dynamical modelling of (bio) molecules using …

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD)
simulations generally relies on a thermodynamic cycle in which the ligand is alchemically …

The simulation of physical systems requires a simplified, hierarchical approach which
models each level from the atomistic to the macroscopic scale. From quantum mechanics to …

A GROMOS force-field parameter set 54A8 is developed, which is based on the latest 54A7
set [Schmid et al. Eur. Biophys. J. 2011, 40, 843–856] and involves a recalibration of the …

A companion article has been published: Computation of methodology-independent single-
ion solvation properties from molecular simulations. III. Correction terms for the solvation free …

The raw ionic solvation free energies computed from atomistic (explicit-solvent) simulations
are extremely sensitive to the boundary conditions (finite or periodic system, system shape …

We present a combined fluctuating charges–polarizable continuum model approach to
describe molecules in solution. Both static and dynamic approaches are discussed …