Berk Hess

Research topics

• Protein Structure and Dynamics · 4 papers
• Machine Learning in Materials Science · 2 papers
• Advanced Chemical Physics Studies · 1 paper
• Spectroscopy and Quantum Chemical Studies · 1 paper
• Matrix Theory and Algorithms · 1 paper
• Parallel Computing and Optimization Techniques · 1 paper

Frequent co-authors

• David van der Spoel · 3 papers
• Erik R. Lindahl · 3 papers
• Herman J. C. Berendsen · 2 papers
• Gerrit Groenhof · 1 paper
• Alan Edward Mark · 1 paper
• Henk Bekker · 1 paper
• J. G. E. M. Fraaije · 1 paper
• Carsten Kutzner · 1 paper

Papers

1. GROMACS: Fast, flexible, and freeJournal of Computational Chemistry · 2005 · 19,704 citations

   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…

2. LINCS: A linear constraint solver for molecular simulationsJournal of Computational Chemistry · 1997 · 17,549 citations

   In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation…

3. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationJournal of Chemical Theory and Computation · 2008 · 16,231 citations

   Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors…

4. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkitBioinformatics · 2013 · 7,748 citations

   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…