Adun: high performance productivity molecular simulations code

ObjectivesAdun is a new extendible molecular simulation program that also includes data management and analysis capabilities. What follows is an overview of our main aims for the 1.0 version of our software. The current stable version is 0.81. For information on the specific features of each release see the Status section.DescriptionThe Adun molecular simulation application has been designed from the ground up to cater for a broad range of users and needs, from computational chemists to experimental biologists. Adun provides advanced algorithms and protocols for molecular simulation which can be accessed from an intuitive user interface but also from a more flexible programmatic level. It is built on the Adun framework which is a powerful library for creating and manipulating simulations. However it goes beyond just performing simulations by incorporating tools for analysis and management of simulation data aswell as providing mechanisms that allow the easy extension of its abilities. In many senses Adun is simply a structure that can incorporate any molecular simulation tools allowing it almost unlimited potential for growth.Innovative AspectsData analysis features are extendible through plugins.Control of a simulation can also be handled by plugins.AdunKernel library provides a high level interface for creating, controlling and manipulating simulationsThe basic libraries are scriptable.Scripts can also run in the context of the running program e.g. Interact with live objects, automated common tasks etc.Tightly integrated with a graphical user interface.Data management features allows browsing, searching and grouping of various types of simulation data.Data storage can be augmented through SQL databases allowing distributed data sharing.Force Field independent – Adun is not coupled to any one force field and it can be extended to use any existing force field (aswell as new ones)AdvantagesAdun seeks to eliminate two of the barriers to productivity that exist with current simulation packages.High Perfomance ProductivityThe plugin & scripting capabilities coupled with the rigorous structure of the Adun framework allow for rapid implementation of new protocols and features. Moreover the implementation and distribution of these features is not tied to the main Adun distribution. New plugins and scripts can be uploaded by developers anywhere to the Adun website and thus users can benefit immediately from them.Data managementMany current simulators leave managing their inputs and output to the user. However raw simulation data and subsequent data derived from it can have complex inter-relationships (between themselves and with the output of other simulations). Keeping track and accessing all this data is a time consuming and difficult task – a burden which Adun removes from the user. However Adun goes beyond data management as it can be augmented through the use of SQL databases. Not only does this provide more advanced storage solutions it also allows browsing and manipulation of Adun data residing in remote databases. This expands the amount of data available for analysis aswell as allowing collaboration through a single interface. <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=416#pack_687">Adun 0.81 </a> : tar ball of the last stable distributionSorce code available at https://gna.org/projects/adun </li> </ul>

Adun是一款新型的可扩展分子模拟程序，同时具备数据管理和分析功能。以下是对本软件1.0版本主要目标的概述。当前稳定版本为0.81。有关每个发布版本的特定功能，请参阅状态部分。

描述：Adun分子模拟应用程序从底层设计，旨在满足从计算化学家到实验生物学家等广泛用户和需求。Adun提供了先进的分子模拟算法和协议，用户可通过直观的用户界面或更灵活的程序级别访问。它基于Adun框架构建，这是一个用于创建和操作模拟的强大库。然而，Adun不仅仅局限于执行模拟，它还集成了分析和管理模拟数据工具，并提供易于扩展其能力的机制。在许多方面，Adun本质上是一个可以整合任何分子模拟工具的结构，使其几乎具有无限的增长潜力。

创新点：
数据分析功能可通过插件进行扩展。
模拟控制也可由插件处理。
AdunKernel库提供了创建、控制和操作模拟的高级接口。
基本库是可脚本化的。
脚本也可以在运行程序的环境中运行，例如与实时对象交互、自动化常见任务等。
与图形用户界面紧密集成。
数据管理功能允许浏览、搜索和分组各种类型的模拟数据。
数据存储可以通过SQL数据库进行增强，从而实现分布式数据共享。
力场独立——Adun不耦合于任何特定的力场，它可以扩展以使用任何现有的力场（以及新的力场）。
优点：
Adun旨在消除当前模拟软件包中存在的两个生产力障碍。
高性能生产力：
插件和脚本功能与Adun框架的严谨结构相结合，允许快速实现新的协议和功能。此外，这些功能的实现和分发并不依赖于Adun的主要分发。开发者可以在Adun网站上上传新的插件和脚本，因此用户可以立即从中受益。
数据管理：
许多当前的模拟器将输入和输出的管理留给用户。然而，原始模拟数据和由此产生的数据可能具有复杂的相互关系（与自身以及与其他模拟输出的关系）。跟踪和访问所有这些数据是一项耗时且困难的任务——Adun从用户那里移除了这一负担。然而，Adun的数据管理功能不仅限于管理，它还可以通过使用SQL数据库进行增强。这不仅提供了更高级的存储解决方案，还允许浏览和操作存储在远程数据库中的Adun数据。这扩大了可用于分析的数据量，同时也允许通过单个界面进行协作。

本项目包括以下软件/数据包：

<ul>
<li><a href="https://simtk.org/frs?group_id=416#pack_687">Adun 0.81</a>：最后稳定分发的tar包。源代码可在https://gna.org/projects/adun获取。</li>
</ul>