Molecular dynamics simulations have become a standard tool for the investigation of
biomolecules. Simulations are performed of ever bigger systems using more realistic boundary …

Successive parameterizations of the GROMOS force field have been used successfully to
simulate biomolecular systems over a long period of time. The continuing expansion of …

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 …

Accurate ligand-protein binding affinity prediction, for a set of similar binders, is a major
challenge in the lead optimization stage in drug development. In general, docking and scoring …

The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb ) is a
Web-accessible server that can provide topologies and parameters for a wide range of …

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 of …

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 …

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 …

The performance of the GROMOS96 parameter set 45A3 developed for aliphatic alkanes is
tested on a bilayer of dipalmitoylphosphatidylcholine (DPPC) in water in the liquid-crystalline …

GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics
simulation trajectories and as such is part of the GROningen MOlecular Simulation software for …