Efficient generation of self-avoiding, semiflexible rotational isomeric chain ensembles in bulk, in confined geometries, and on surfaces

We provide an efficient ready-to-run code gensaw that generates single or large ensembles of self-avoiding, flexible, semiflexible, rotationally isometric or helical chains in the bulk or subject to arbitrary confinement and tethering conditions, where we allow for arbitrary intramolecular bending and dihedral energy functions. The resulting configuration files are provided in various common formats and can be immediately used to do molecular simulations or statistical analysis. We work out analytic expressions for the mean squared end-to-end distance and gyration radius of the semiflexible, helical and rotational isomeric state models with a finite number of bonds and arbitrary interaction potentials for direct comparison and testing of the code in the limiting case of unconfined phantom chains. In addition to the graphics-free linux standalone batch version gensaw that creates configuration and other files for high throughput applications from the command line, we provide an interactive online version gensaw-visualization that serves as platform-independent graphical user interface, and animates the resulting conformations using a remote gensaw server.

我们研发了一款高效可直接运行的代码工具gensaw，可生成单条或大规模集合的自规避（self-avoiding）、柔性、半柔性、旋转等距（rotationally isometric）或螺旋聚合物链，既支持本体环境下的构建，也可适配任意受限与锚定条件，同时允许自定义分子内弯曲与二面角能量函数。生成的构型文件支持多种通用格式，可直接用于分子模拟或统计分析。针对有限键数、自定义相互作用势的半柔性、螺旋及旋转异构态（rotational isomeric state）模型，我们推导了其均方末端距与回转半径（radius of gyration）的解析表达式，可用于无受限幻影链极限场景下的代码验证与直接对比测试。除了面向命令行高通量应用、可生成构型及其他文件的无图形界面Linux独立批处理版本gensaw外，我们还提供了交互式在线版本gensaw-visualization：该版本为跨平台图形用户界面，可通过远程gensaw服务器对生成的构象进行动画可视化展示。