1Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden, 2Dept. Theoretical Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden, 3 Theoretical and Computational Biophysics Dept., Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany 4Center for Biomembrane Research, Dept. Biochemistry & Biophysics, Stockholm University, SE...

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...

We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling even on such clusters with only limited bandwidth and high latency. GROMACS 3.3 scales well on supercomputers like the IBM p690 (Regatta) and on Linux clusters with a special interconnect like Myrinet or Infiniband. Because of the high s...

MOTIVATION Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to mo...

A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro)molecules in aqueous environment is described. The software has been developed for a custom-designed 32-processor ring GROMACS (GROningen MAchine for Chemical Simulation) with communication to and from left and right neighbours, but can mn on any parallel system onto which a a ring of pro...

A novel protocol has been developed for comparing the structural properties of lipid bilayers determined by simulation with those determined by diffraction experiments, which makes it possible to test critically the ability of molecular dynamics simulations to reproduce experimental data. This model-independent method consists of analyzing data from molecular dynamics bilayer simulations in the...

Gradients in free energies are the driving forces of physical and biochemical systems. To predict energy differences with high accuracy, Molecular Dynamics (MD) other methods based on atomistic Hamiltonians conduct sampling simulations intermediate thermodynamic states that bridge configuration space densities between two interest ('alchemical transformations'). For uncorrelated sampling, recen...