PLUMED 2: New feathers for an old bird
PLUMED 2: New feathers for an old bird
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DOI：
10.1016/j.cpc.2013.09.018
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发表时间：
2014-02-01
影响因子：
6.3
通讯作者：
Bussi, Giovanni
中科院分区：
文献类型：
--
作者：
Tribello, Gareth A.;Bonomi, Massimiliano;Bussi, Giovanni
加强采样和分析模拟是分子模拟的核心问题。最近，我们介绍了一个开源插件Pleed，它提供了一些最流行的分子动力学(MD)代码，并实现了各种不同的增强采样算法和集合变量(CV)。这一领域的快速变化，特别是在增强采样和降维方面的新方向，以及新的硬件，需要更灵活和更有效的代码。因此，我们在这里展示了一种用面向对象编程语言(C++)对代码进行完全重写的Plefed 2。这个新版本引入了更大的灵活性和更大的模块化，这既扩展了其核心功能，又使添加新方法和CV变得更加容易。它还与MD引擎有一个更简单的接口，并提供包含工具和核心设施的单一软件库。最终，新代码更好地服务于不断增长的用户和贡献者社区，以应对该领域出现的新挑战。计划摘要计划标题：Pleed 2目录标识符：AEEE_v2_0计划摘要URL：http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.htmlProgram可从：爱尔兰贝尔法斯特女王大学CPC程序图书馆获得许可条款：Yesno。分布式程序中的行数，包括测试数据等：700646号分布式程序中的字节数，包括测试数据等：6618136分布格式：tar.gz编程语言：ansi-C++计算机：任何能够运行由C++编译器产生的可执行文件的计算机。操作系统：Linux操作系统，Unix OS。代码是否被矢量化或并行化？：是，用MPI.RAM并行化：取决于原子数、选择的方法和使用的集合变量。分类：3、7.7、23。前一版本的目录标识：AEEE_v1_0。前一版本的日记账引用：COMPUT。太棒了。通讯。180(2009)196.外部例程：GNU libmatheval，Lapack，Bias，MPI。(C)2013爱思唯尔B.V.保留所有权利。
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.Program summaryProgram title: PLUMED 2Catalogue identifier: AEEE_v2_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: YesNo. of lines in distributed program, including test data, etc.: 700646No. of bytes in distributed program, including test data, etc.: 6618136Distribution format: tar.gzProgramming language: ANSI-C++.Computer: Any computer capable of running an executable produced by a C++ compiler.Operating system: Linux operating system, Unix OSs.Has the code been vectorized or parallelized?: Yes, parallelized using MPI.RAM: Depends on the number of atoms, the method chosen and the collective variables used.Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.