GROMACS 3.0: a package for molecular simulation and trajectory analysis

TL;DR: A multiscale investigation of the bulk and surface of aqueous electrolyte solutions that extends from the atomic scale to nanoscopic length scales (using bulk and interfacial femtosecond second harmonic measurements) to the macroscopic scale (using surface tension experiments).

TL;DR: A large-scale replica exchange molecular dynamics simulation that provides extensive sampling of the entire ensemble of oligonucleotide conformations in a (GT)(7)-SWCN hybrid expands the understanding of DNA-CN and indicates the relevance of REMD for explorations of the physical properties of organic-inorganic multifunctional nanomaterials.

TL;DR: The unprecedented detail of the NMR data enables a more complete comparison between simulations and experiments on POPC-cholesterol bilayers and may aid in developing more realistic model descriptions of biological membranes.

TL;DR: This work presents a method, implemented within the MD package GROMACS, for constant pH molecular dynamics simulations in explicit solvent that is based on the λ-dynamics approach, which allows the protonated states of titratable groups to change dynamically during a simulation, thus reproducing average protonation probabilities at a certain pH.

TL;DR: In this paper, a simulation program for particle-mesh force calculation is presented, based on a one-dimensional plasma model and a collisionless particle model, which is used to simulate collisionless particle models.

Abstract: The structures of the three major classes of biopolymers-polynucleotides, polypeptides and polysaccharides-are surveyed in the light of the most recent results from X-ray diffraction, electron microscopy and other studies. The review contains an introductory section setting out the basic features of each class of biopolymer: the natures of the 'building blocks', the linkages between them, conformational principles, types of repeating (secondary) structures and so on. The main section on each class is deliberately selective, because of the large amount of structural information now available. The section on polynucleotides concentrates on DNA, reviewing the classical double-helical models and the evidence provided by X-ray fibre diffraction, but also paying special attention to the rapid growth of new information on such features as the variations in helix geometry and in base-stacking, those data being derived primarily from studies of small self-complementary oligonucleotides. Alternative models and the question of right-handed versus left-handed structures are also considered. Among polypeptide structures, both globular and fibrous proteins are described. Globular proteins are treated as a group, with no detailed description of any one of them; this section concentrates on the organisation of globular proteins via folding units and domains, some general features (protein homology, catalysis, flexibility, interaction with water), membrane proteins, immunoglobulins and viruses.

TL;DR: A comparison of a series of extended molecular dynamics simulations of bacteriophage T4 lysozyme in solvent with X‐ray data is presented, revealing that the N‐terminal helix rotates together with either of these two domains.