This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

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GROMACS: Fast, flexible, and free

GROMACS: A message-passing parallel molecular dynamics implementation

Theory of electroporation: A review

The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. Genetic defects in ClC Cl- channels underlie several familial muscle and kidney diseases. Here we present the X-ray structures of two prokaryotic ClC Cl- channels from Salmonella enterica serovar typhimurium and Escherichia coli at 3.0 and 3.5 A, respectively. Both structures reveal two identical pores, each pore being formed by a separate subunit contained within a homodimeric membrane protein. Individual subunits are composed of two roughly repeated halves that span the membrane with opposite orientations. This antiparallel architecture defines a selectivity filter in which a Cl- ion is stabilized by electrostatic interactions with alpha-helix dipoles and by chemical coordination with nitrogen atoms and hydroxyl groups. These findings provide a structural basis for further understanding the function of ClC Cl- channels, and establish the physical and chemical basis of their anion selectivity.

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X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity.

Electric field-mediated fusion and related electrical phenomena.

Relaxation techniques have been widely used in kinetic studies of chemical reactions in homogeneous solution (Eigen & DeMayer, 1963). The principle of this method is well known: an external variable such as temperature or pressure is suddenly changed and the time course of a state parameter of the system such as concentration is recorded as it approaches a new steady value. Relaxation techniques can also be used for studying the rate of elementary processes in membranes. This method has proved particularly useful for the investigation of ion transport systems (ion carriers, channels, pumps) in artificial planar bilayer membranes. In this review we describe different relaxation techniques which have been developed for this purpose during the last years, as well as applications to a number of ion transport systems.

Relaxation studies of ion transport systems in lipid bilayer membranes.

We discuss the equation of state and the static correlations in a system of spherical ferromagnetic grains suspended in a magnetically passive fluid. In the domain where dipole-dipole interactions between the grains are large (low temperature) we show that the variation of the small-angle X-ray scattering with magnetic field provides a sensitive test of the model proposed to treat this system. We discuss the condensation of the grains into linear chains at low density, high magnetic field, and low temperature. The possibility of resonances in the small-angle X-ray scattering is demonstrated and certain other consequences of chain formation are indicated.

Peter C. Jordan

Papers

Relaxation studies of ion transport systems in lipid bilayer membranes.

Association phenomena in a ferromagnetic colloid

Electrostatic modeling of ion pores. Energy barriers and electric field profiles.

How electrolyte shielding influences the electrical potential in transmembrane ion channels.

How pore mouth charge distributions alter the permeability of transmembrane ionic channels.