Ribeiro João V, Bernardi Rafael C, Rudack Till, Stone John E, Phillips James C, Freddolino Peter L, Schulten Klaus
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.
Energy Biosciences Institute, University of Illinois at Urbana-Champaign, USA.
Sci Rep. 2016 May 24;6:26536. doi: 10.1038/srep26536.
The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.
生物分子在活细胞中的正常功能需要它们呈现特定的结构并经历构象变化。生物分子的结构和运动都可以使用多种技术进行研究，但没有一种技术能像分子动力学（MD）模拟那样提供详细程度的信息。整合了两个广泛使用的建模程序，即NAMD和VMD，我们创建了一个强大且用户友好的软件QwikMD，它使新手和专家都能够解决生物医学相关问题，而这些问题往往只有分子动力学模拟才能提供答案。QwikMD以交互方式执行简单和高级的MD模拟，在准备、执行和分析模拟所需的尽可能多的步骤上实现自动化，同时检查常见错误并确保可重复性。QwikMD也满足了该领域专家的需求，通过执行繁琐或重复的任务提高了他们的工作效率和质量，同时使每个步骤都易于控制。无论是在小型笔记本电脑上的实时视图模式下进行模拟，还是在超级计算机或云计算上执行复杂的大型模拟，QwikMD都使用相同的步骤和用户界面。QwikMD可通过在群组和个人计算机上下载免费获取。它也可在亚马逊网络服务的云端使用。
