Tan Robert K Z, Petrov Anton S, Harvey Stephen C
School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, Georgia 30332.
J Chem Theory Comput. 2006 May 1;2(3):529-540. doi: 10.1021/ct050323r. Epub 2006 Mar 18.
Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multi-scaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual non-linear polymer and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsid. We find that objects are easy to modify, extend and redeploy. Thus, new classes of coarse-grained models can be implemented easily.
粗粒度模型可能与全原子模型有很大不同，并且种类繁多。每一类模型的组装方式都大不相同，有些模型需要标准分子力学方法的定制版本。满足这些多样需求的最灵活方式是提供对内部数据结构的访问以及一种用于操作这些结构的编程语言。我们创建了YUP，一个用于粗粒度和多尺度模型的通用程序。YUP通过添加新的数据类型扩展了Python编程语言。然后我们使用扩展后的语言实现了三类粗粒度模型。粗粒度RNA模型类型是一种不寻常的非线性聚合物，用一个简单的程序就能轻松处理其组装。对于粗粒度DNA模型，分子动力学算法必须进行扩展，以便它能够检测到标准实现中不可见的故障。第三种模型类型利用对力场的访问来模拟病毒衣壳中DNA的堆积。我们发现对象易于修改、扩展和重新部署。因此，可以轻松实现新的粗粒度模型类别。
