A domain decomposition molecular dynamics program for the simulation of flexible molecules with an arbitrary topology of Lennard-Jones and/or Gay-Berne sites

Jaroslav Ilnytskyi; Mark R. Wilson

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A domain decomposition molecular dynamics program for the simulation of flexible molecules with an arbitrary topology of Lennard-Jones and/or Gay-Berne sites

机译：域分解分子动力学程序，用于模拟具有Lennard-Jones和/或Gay-Berne位点的任意拓扑的柔性分子

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We describe a new parallel molecular dynamics program GBMOLDD which uses the domain decomposition algorithm. The program is designed to simulate molecular systems composed of both spherically-symmetric and anisotropic sites connected via arbitrary topology and described by standard force fields. The program is oriented mainly towards simulations of liquid crystalline systems including mixtures of mesogenic molecules and mesogens confined in host media. Benchmark results are presented for a model liquid crystal dimer composed of two mesogenic units linked via a flexible alkyl chain. The benchmarks compare favorably to those obtained via a parallel replicated data algorithm.

机译：我们描述了一种新的平行分子动力学程序GBMOLDD，它使用域分解算法。该程序旨在模拟由任意对称拓扑连接并由标准力场描述的球形对称和各向异性位点组成的分子系统。该程序主要面向模拟液晶系统，包括介晶分子和限定在宿主介质中的介晶混合物。给出了由两个通过柔性烷基链连接的介晶单元组成的液晶二聚体模型的基准结果。这些基准与通过并行复制数据算法获得的基准相比具有优势。

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《Computer physics communications》 |2001年第1期|共10页
作者
Jaroslav Ilnytskyi; Mark R. Wilson;
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正文语种 eng
中图分类计算机的应用;
关键词
molecular dynamics; atomistic simulations; parallel computing; domain decomposition; liquid crystals;

机译：分子动力学;原子模拟;并行计算;畴分解;液晶;

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1. A domain decomposition molecular dynamics program for the simulation of flexible molecules with an arbitrary topology of Lennard-Jones and/or Gay-Berne sites [J] . Jaroslav Ilnytskyi, Mark R. Wilson Computer physics communications . 2001,第1期

机译：域分解分子动力学程序，用于模拟具有Lennard-Jones和/或Gay-Berne位点的任意拓扑的柔性分子
2. A domain decomposition molecular dynamics program for the simulation of flexible molecules of spherically-symmetrical and nonspherical sites. II. Extension to NVT and NPT ensembles [J] . Jaroslav M. Ilnytskyi, Mark R. Wilson Computer physics communications . 2002,第1期

机译：域分解分子动力学程序，用于仿真球形对称和非球形部位的柔性分子。二。扩展到NVT和NPT集成
3. A domain decomposition molecular dynamics program for the simulation of flexible molecules of spherically-symmetrical and nonspherical sites. II. Extension to NVT and NPT ensembles [J] . Jaroslav M. Ilnytskyi, Mark R. Wilson Computer physics communications . 2002,第1期

机译：域分解分子动力学程序，用于仿真球形对称和非球形部位的柔性分子。二。扩展到NVT和NPT集成
4. MOLECULAR DYNAMICS SIMULATIONS OF HMX CRYSTAL POLYMORPHS USING A FLEXIBLE MOLECULE FORCE FIELD [C] . Dmitry Bedrov, Grant D. Smith, Thomas D. Sewell Shock Compression of Condensed Matter―2001 . 2002

机译：使用柔性分子场模拟HMX晶体的分子动力学
5. Molecular dynamics simulation of interfacial tension and contact angle of Lennard-Jones fluid. [D] . Sinha, Shashank. 2004

机译：Lennard-Jones流体界面张力和接触角的分子动力学模拟。
6. Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations [O] . Lina Kulakova, Georgios Arampatzis, Panagiotis Angelikopoulos, -1

机译：分子动力学模拟中Lennard-Jones势斥力指数的数据驱动推论
7. A Domain Decomposition Parallel Processing Algorithm for Molecular Dynamics Simulations of Systems of Arbitrary Connectivity. [O] . David Brown, Hervé Minoux, Bernard Maigret 1997

机译：任意连通系统分子动力学模拟的区域分解并行处理算法。

A domain decomposition molecular dynamics program for the simulation of flexible molecules with an arbitrary topology of Lennard-Jones and/or Gay-Berne sites

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