scispace - formally typeset
Author

Berk Hess

Bio: Berk Hess is a academic researcher from Royal Institute of Technology. The author has contributed to research in topic(s): Molecular dynamics & Wetting. The author has an hindex of 36, co-authored 76 publication(s) receiving 61326 citation(s). Previous affiliations of Berk Hess include Stockholm University & Imperial College London.

...read more

Topics: Molecular dynamics, Wetting, SIMD ...read more
Papers
  More

Open accessJournal ArticleDOI: 10.1021/CT700301Q
Abstract: 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 from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

...read more

  • Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
    Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
  • Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
    Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
  • Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
    Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
  • Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
    Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
  • Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
    Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
  • + 2

Topics: Particle Mesh (50%)

12,609 Citations


Journal ArticleDOI: 10.1002/JCC.20291
David van der Spoel1, Erik Lindahl2, Berk Hess3, Gerrit Groenhof4  +2 moreInstitutions (4)
Abstract: 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.

...read more

Topics: Software suite (50%)

10,642 Citations


Abstract: 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 of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. (C) 1997 John Wiley & Sons, Inc.

...read more

10,230 Citations


Open accessJournal ArticleDOI: 10.1016/J.SOFTX.2015.06.001
Mark Abraham1, Teemu Murtola2, Roland Schulz3, Roland Schulz4  +6 moreInstitutions (4)
01 Sep 2015-SoftwareX
Abstract: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, prepa ...

...read more

8,050 Citations


Journal ArticleDOI: 10.1007/S008940100045
Abstract: GROMACS 3.0 is the latest release of a versatile and very well optimized package for molecular simulation. Much effort has been devoted to achieving extremely high performance on both workstations and parallel computers. The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x–1/2. Inner loops are generated automatically in C or Fortran at compile time, with optimizations adapted to each architecture. Assembly loops using SSE and 3DNow! Multimedia instructions are provided for x86 processors, resulting in exceptional performance on inexpensive PC workstations. The interface is simple and easy to use (no scripting language), based on standard command line arguments with self-explanatory functionality and integrated documentation. All binary files are independent of hardware endian and can be read by versions of GROMACS compiled using different floating-point precision. A large collection of flexible tools for trajectory analysis is included, with output in the form of finished Xmgr/Grace graphs. A basic trajectory viewer is included, and several external visualization tools can read the GROMACS trajectory format. Starting with version 3.0, GROMACS is available under the GNU General Public License from http://www.gromacs.org.

...read more

Topics: Compile time (51%), Command-line interface (51%)

6,008 Citations


Cited by
  More

Open access
Steven J. Plimpton1Institutions (1)
01 May 1993-
Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

...read more

Topics: Intel Paragon (64%), Intel iPSC (62%), Parallel algorithm (58%)

24,496 Citations


Open accessJournal ArticleDOI: 10.1021/CT700301Q
Abstract: 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 from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

...read more

  • Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
    Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
  • Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
    Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
  • Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
    Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
  • Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
    Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
  • Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
    Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
  • + 2

Topics: Particle Mesh (50%)

12,609 Citations


Journal ArticleDOI: 10.1002/JCC.20291
David van der Spoel1, Erik Lindahl2, Berk Hess3, Gerrit Groenhof4  +2 moreInstitutions (4)
Abstract: 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.

...read more

Topics: Software suite (50%)

10,642 Citations


Open accessJournal ArticleDOI: 10.1016/J.SOFTX.2015.06.001
Mark Abraham1, Teemu Murtola2, Roland Schulz3, Roland Schulz4  +6 moreInstitutions (4)
01 Sep 2015-SoftwareX
Abstract: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, prepa ...

...read more

8,050 Citations


Open accessJournal ArticleDOI: 10.1002/JCC.21287
Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

...read more

5,997 Citations


Performance
Metrics

Author's H-index: 36

No. of papers from the Author in previous years
YearPapers
20211
20204
20194
20184
20175
20161

Top Attributes

Show by:

Author's top 5 most impactful journals

Journal of Chemical Physics

11 papers, 967 citations

Journal of Physical Chemistry B

5 papers, 431 citations

Macromolecules

4 papers, 72 citations

Biophysical Journal

4 papers, 173 citations

Network Information
Related Authors (5)
Teemu Murtola

5 papers, 8.4K citations

86% related
Szilárd Páll

16 papers, 14.7K citations

83% related
Andreas Beckmann

20 papers, 222 citations

81% related
Erik Lindahl

174 papers, 54.9K citations

80% related
Mark Abraham

17 papers, 9.3K citations

80% related