Centre de Biophysique Moléculaire (CNRS), Rue Charles Sadron, 45071 Orléans, France.
J Comput Chem. 2012 Sep 30;33(25):2043-8. doi: 10.1002/jcc.23035. Epub 2012 Jun 8.
We present a new version of the program package nMoldyn, which has been originally developed for a neutron-scattering oriented analysis of molecular dynamics simulations of macromolecular systems (Kneller et al., Comput. Phys. Commun. 1995, 91, 191) and was later rewritten to include in-depth time series analyses and a graphical user interface (Rog et al., J. Comput. Chem. 2003, 24, 657). The main improvement in this new version and the focus of this article are the parallelization of all the analysis algorithms for use on multicore desktop computers as well as distributed-memory computing clusters. The parallelization is based on a task farming approach which maintains a simple program structure permitting easy modification and extension of the code to integrate new analysis methods.
我们提出了一个新版本的程序包 nMoldyn，它最初是为了对大分子系统的分子动力学模拟进行面向中子散射的分析而开发的（Kneller 等人，Comput. Phys. Commun. 1995, 91, 191），后来被重写为包括深入的时间序列分析和图形用户界面（Rog 等人，J. Comput. Chem. 2003, 24, 657）。这个新版本的主要改进和本文的重点是所有分析算法的并行化，以便在多核台式计算机以及分布式内存计算集群上使用。并行化基于任务农场方法，该方法保持了简单的程序结构，允许轻松修改和扩展代码以集成新的分析方法。
