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 compute...
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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://***.
Results of several parallel molecular dynamics crack simulations in bcc iron crystals with up to 128 million atoms are presented. The crack (001)[010] of Griffith type is loaded in Mode I. We observe dislocation emiss...
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ISBN:
(纸本)0878499644
Results of several parallel molecular dynamics crack simulations in bcc iron crystals with up to 128 million atoms are presented. The crack (001)[010] of Griffith type is loaded in Mode I. We observe dislocation emission and twinning near the free sample surfaces and later plastically induced crack initiation.
In this Article, a review is given on the progress of simulating complex fluids. Two approaches are used to deal with the special requirements of simulations of complex fluids. moleculardynamics on massively parallel...
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In this Article, a review is given on the progress of simulating complex fluids. Two approaches are used to deal with the special requirements of simulations of complex fluids. moleculardynamics on massively parallel computers allow long simulations on very large systems. This makes it possible to simulate the self-assembly of micelles and the solubilization of a droplet of oil. For problems in which dynamics is not essential, it is shown that a novel method, configurational-bias Monte Carlo, can be used to simulate efficiently systems containing chain molecules. The use of this method is illustrated by a calculation of the vapour-liquid curve of an alkane as long as octatetracontane C-48.
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