PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
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DOI：
10.1021/ct400341p
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发表时间：
2013-07-01
影响因子：
5.5
通讯作者：
Cheatham, Thomas E., III
中科院分区：
文献类型：
--
作者：
Roe, Daniel R.;Cheatham, Thomas E., III
我们描述了PTRAJ和它的后继者CPPTRAJ，这两个互补的、便携式的和免费可用的计算机程序用于分析和处理三维原子位置的时间序列（即，坐标轨迹）和其中导出的数据。常见工具包括操纵数据以在轨迹格式之间转换的能力，处理用集合方法生成的轨迹组（例如，复制交换分子动力学），使用周期性边界条件成像，创建平均结构，剥离系统子集，并执行计算，如RMS拟合，测量距离，B因子，回转半径，径向分布函数和时间相关性，以及其他操作和分析。PTRAJ和CPPTRAJ程序和源代码都可以在GNU通用公共许可证第3版下免费获得，目前在AmberTools 12支持程序套件中分发，该套件构成了Amber计算机程序包的一部分（参见http://ambermd.org）。本概述介绍了这两个程序的总体设计、功能和历史;以及CPPTRAJ中可用的算法改进和新功能。
We describe PTRAJ and its, successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions,create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (See http://ambermd.org). This overview describes the general design, features, and history of these two programs; as well as algorithmic improvements and new features available in CPPTRAJ.