Roopra Sanjit, Knapp Bernhard, Omasits Ulrich, Schreiner Wolfgang
Department of Bioinformatics, Upper Austrian University of Applied Sciences, Softwarepark 11 4232 Hagenberg, Austria.
J Chem Inf Model. 2009 Oct;49(10):2412-7. doi: 10.1021/ci900248f.
Molecular dynamics (MD) is a technique to simulate movements of molecular structures to understand their functional behavior. GROMACS is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. This makes it powerful but also complicated to handle. We introduce jSimMacs, a Java application for creating molecular dynamics projects in GROMACS. It simplifies the handling of files and options via an intuitive user interface. Users unexperienced in MD can work along prepared lines, while experts may enjoy a significant relief from the tedium of typing and scripting. Furthermore, jSimMacs supports 3D interactivity and the launch of remote projects on other computers accessible via networks. Thus, jSimMacs not only opens GROMACS to a broader public but also eases the burden of performing series of MD runs, as necessary in parameter studies.
分子动力学（MD）是一种模拟分子结构运动以了解其功能行为的技术。GROMACS是一个主要为生物分子动力学开发的软件包，它提供了大量用于定制模拟的可能选项和设置。这使得它功能强大，但操作起来也很复杂。我们介绍jSimMacs，一个用于在GROMACS中创建分子动力学项目的Java应用程序。它通过直观的用户界面简化了文件和选项的处理。没有分子动力学经验的用户可以按照准备好的步骤进行操作，而专家们则可以从繁琐的打字和脚本编写中大大解脱出来。此外，jSimMacs支持3D交互性以及在通过网络可访问的其他计算机上启动远程项目。因此，jSimMacs不仅向更广泛的公众开放了GROMACS，还减轻了在参数研究中进行一系列分子动力学运行的负担。
