Change search
Refine search result
1 - 6 of 6
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Abraham, Mark J
    Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, Australia.
    Performance enhancements for GROMACS nonbonded interactions on BlueGene.2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9Article in journal (Refereed)
    Abstract [en]

    Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table look-ups. Some other GROMACS simulations will show a small gain.

  • 2.
    Abraham, Mark J
    et al.
    Australian National University, Australia.
    Gready, Jill E
    Australian National University.
    Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 7Article in journal (Refereed)
    Abstract [en]

    We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) simulations that make efficient use of the replica space, assess whether published applications are achieving such "mixing" efficiency, and provide a how-to guide to assist users to plan efficient REMD simulations. To address our first question, we introduce and discuss three metrics for assessing the number of replica-exchange attempts required to justify the use of a replica scheme and define a "transit number" as the lower bound for the length of an efficient simulation. Our literature survey of applications of REMD simulations of peptides in explicit solvent indicated that authors are not routinely reporting sufficient details of their simulation protocols to allow readers to make independent assessments of the impact of the method on their results, particularly whether mixing efficiency has been achieved. Necessary details include the expected or observed replica-exchange probability, together with the total number of exchange attempts, the exchange period, and estimates of the autocorrelation time of the potential energy. Our analysis of cases where the necessary information was reported suggests that in many of these simulations there are insufficient exchanges attempted or an insufficiently long period between them to provide confidence that the simulation length justifies the size of the replica scheme. We suggest guidelines for designing REMD simulation protocols to ensure mixing efficiency. Two key recommendations are that the exchange period should in general be larger than 1 ps and the number of exchange attempts should be chosen to significantly exceed the transit number for the replica scheme.

  • 3.
    Abraham, Mark J
    et al.
    Australian National University, Australia.
    Gready, Jill E
    Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.52011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9Article in journal (Refereed)
    Abstract [en]

    Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle-mesh Ewald (PME) implementation in GROMACS 4.5, we present a computational tool to enable the discovery of parameters that produce a given accuracy in the PME approximation of the full electrostatics. Calculations on two parallel computers with different processor and communication structures showed that a given accuracy can be attained over a range of parameter space, and that the attributes of the hardware and simulation system control which parameter sets are optimal. This information can be used to find the fastest available PME parameter sets that achieve a given accuracy. We hope that this tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade-off between cost and scientific reliability in biomolecular applications.

  • 4.
    Abraham, Mark James
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Physics, Theoretical Biological Physics.
    Murtola, Teemu
    Schulz, Roland
    Pall, Szilard
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Physics, Theoretical Biological Physics.
    Smith, Jeremy C.
    Hess, Berk
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Physics, Theoretical Biological Physics.
    Lindahl, Erik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Physics, Theoretical Biological Physics.
    GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers2015In: SoftwareX, E-ISSN 2352-7110, Vol. 1-2, p. 19-25Article in journal (Refereed)
    Abstract [en]

    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, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.

  • 5.
    Páll, Szilard
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Abraham, Mark James
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kutzner, Carsten
    Hess, Berk
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Biochemistry & Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden .
    Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS2015In: Solving software challenges for exascale, Springer Publishing Company, 2015, p. 3-27Conference paper (Refereed)
    Abstract [en]

    GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.

  • 6.
    Wennberg, Christian L.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Murtola, Teemu
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pall, Szilard
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Abraham, Mark James
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 12, p. 5737-5746Article in journal (Refereed)
    Abstract [en]

    Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecular simulation performance that is an order of magnitude faster than any other available lattice summation technique for LJ interactions. The implementation includes both CPU and GPU acceleration, and its combination with improved scaling LJ-PME simulations now provides performance close to the truncated potential methods in GROMACS but with much higher accuracy.

1 - 6 of 6
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf