The Experts below are selected from a list of 37563 Experts worldwide ranked by ideXlab platform
Erik Lindahl - One of the best experts on this subject based on the ideXlab platform.
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gromacs 4 algorithms for highly efficient load balanced and scalable Molecular Simulation
Journal of Chemical Theory and Computation, 2008Co-Authors: Berk Hess, David Van Der Spoel, Carsten Kutzner, Erik LindahlAbstract: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...
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GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable Molecular Simulation
Journal of Chemical Theory and Computation, 2008Co-Authors: Berk Hess, David Van Der Spoel, Carsten Kutzner, Erik LindahlAbstract: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...
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gromacs 3 0 a package for Molecular Simulation and trajectory analysis
Journal of Molecular Modeling, 2001Co-Authors: Erik Lindahl, Berk Hess, David Van Der SpoelAbstract: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.
Erich A. Müller - One of the best experts on this subject based on the ideXlab platform.
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Molecular Simulation of Adsorption of Gases on Nanotubes
Adsorption and Phase Behaviour in Nanochannels and Nanotubes, 2020Co-Authors: Erich A. MüllerAbstract:Molecular Simulation poses a unique advantage as a technique to understand the physical phenomena at the nanoscale, as it provides an utmost level of control over the relevant variables. The available Molecular Simulation methods for the modelling of adsorption of gases in single-walled carbon nanotubes are reviewed. Special emphasis is given to the adsorption of low Molecular weight gases within classical (non-quantum) scenarios and an overview of commonly employed interMolecular potentials, methodologies and recent results is provided. While the adsorption characteristics of fluids on nanotubes have some parallels with other carbon adsorbents, their one-dimensional morphology contributes to some of the unique adsorption properties described here. Additionally, the effect of interstitial and exohedral adsorption is discussed.
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Purification of water through nanoporous carbon membranes: A Molecular Simulation viewpoint
Current Opinion in Chemical Engineering, 2013Co-Authors: Erich A. MüllerAbstract:Although carbon is generally considered hydrophobic and a poor choice to fabricate membranes, recent developments in nanotechnology have provided nanoporous structures such as nanotubes and graphene sheets, which hold promise as the 'ultimate' membrane materials for water purification. Nonetheless, the behaviour of water through these nanoconfined environments is unique and nonintuitive. This review describes our current understanding and challenges associated with the Molecular Simulation of the water-carbon interaction. It is expected that Simulations can guide the design of water purification membranes with both high selectivity and high permeability. © 2013 Elsevier Ltd.
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Molecular Simulation of Joule–Thomson Inversion Curves
International Journal of Thermophysics, 1999Co-Authors: Coray M. Colina, Erich A. MüllerAbstract:A method to determine Joule–Thomson inversion curves, using isobaric-isothermal Monte Carlo Molecular Simulations, is presented. The usual experimental practice to obtain the locus of points in which the isenthalpic derivative of temperature with respect to pressure vanishes is to process volumetric data by means of thermodynamic relations. This experimental procedure requires the very precise measurement of volumetric properties at conditions up to five times the fluid's critical temperature and twelve times its critical pressure. These harsh experimental conditions have hindered the publication of data for even simple fluids and mixtures. By using Molecular Simulation, these problems may be circumvented, since the computational effort is roughly independent of the actual value of the pressure or the temperature. In general, Joule–Thomson inversion curves obtained by Molecular Simulation may be used either as an unambiguous test for equations of state in the supercritical and high-pressure regions or for the prediction of real fluid behavior, should the potential be well known. Both applications are exemplified for a Lennard-Jones fluid for which the complete inversion curve is obtained.
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JOULE-THOMSON INVERSION CURVES BY Molecular Simulation
Molecular Simulation, 1997Co-Authors: Coray M. Colina, Erich A. MüllerAbstract:Abstract A method to determine Joule-Thomson inversion curves, using isobaric-isothermal Monte Carlo Molecular Simulations, is presented. Volumetric data obtained through the Simulations is interpreted by means of thermodynamic relations to obtain the locus of points in which the isenthalpic derivative of temperature with respect to pressure vanishes. The procedure is exemplified for a Lennard-Jones fluid and the low-temperature branch of the inversion curve is obtained. In general, Joule-Thomson inversion curves obtained by Molecular Simulation may be used either as an unambiguous test for equations of state in the supercritical and high-pressure regions or for the prediction of real fluid behavior, should the potential be well known. Examples of both applications are presented.
Berk Hess - One of the best experts on this subject based on the ideXlab platform.
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gromacs 4 algorithms for highly efficient load balanced and scalable Molecular Simulation
Journal of Chemical Theory and Computation, 2008Co-Authors: Berk Hess, David Van Der Spoel, Carsten Kutzner, Erik LindahlAbstract: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...
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GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable Molecular Simulation
Journal of Chemical Theory and Computation, 2008Co-Authors: Berk Hess, David Van Der Spoel, Carsten Kutzner, Erik LindahlAbstract: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...
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gromacs 3 0 a package for Molecular Simulation and trajectory analysis
Journal of Molecular Modeling, 2001Co-Authors: Erik Lindahl, Berk Hess, David Van Der SpoelAbstract: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.
Carsten Kutzner - One of the best experts on this subject based on the ideXlab platform.
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gromacs 4 algorithms for highly efficient load balanced and scalable Molecular Simulation
Journal of Chemical Theory and Computation, 2008Co-Authors: Berk Hess, David Van Der Spoel, Carsten Kutzner, Erik LindahlAbstract: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...
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GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable Molecular Simulation
Journal of Chemical Theory and Computation, 2008Co-Authors: Berk Hess, David Van Der Spoel, Carsten Kutzner, Erik LindahlAbstract: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...
David Van Der Spoel - One of the best experts on this subject based on the ideXlab platform.
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gromacs 4 algorithms for highly efficient load balanced and scalable Molecular Simulation
Journal of Chemical Theory and Computation, 2008Co-Authors: Berk Hess, David Van Der Spoel, Carsten Kutzner, Erik LindahlAbstract: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...
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GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable Molecular Simulation
Journal of Chemical Theory and Computation, 2008Co-Authors: Berk Hess, David Van Der Spoel, Carsten Kutzner, Erik LindahlAbstract: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...
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gromacs 3 0 a package for Molecular Simulation and trajectory analysis
Journal of Molecular Modeling, 2001Co-Authors: Erik Lindahl, Berk Hess, David Van Der SpoelAbstract: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.
