REWRITING YAMMP

重写YAMMP

• 批准号: 7358856
• 负责人: STEPHEN C. HARVEY
• 金额: $ 7.73万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2007-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7358856
• 关键词: REWRITING; YAMMP

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Yammp is a general purpose molecular mechanics program, initially developed for coarse-grain modeling of macromolecular systems, although we have tackled some all-atom problems with Yammp. It was originally applied to a range of unrelated problems (DNA supercoiling, the structure of the ribosome, and mean-field simulations on model membranes, among others). As demand for coarse-grained models grew, we decided to rewrite Yammp into a form (Yammp2) that would enable it to become an extension of Python. The result is YUP (Yammp Under Python), which has additional data types that are particularly useful for molecular mechanics calculations. YUP (Yammp Under Python) is an extension of Python, with additional data types that are particularly useful for molecular mechanics calculations. YUP is therefore highly programmable, which is its main strength. The user will find, however, that YUP requires more effort to learn than does a traditional molecular mechanics program, where one can build models and run simulations quickly, either from a GUI, or by modifying other people¿s scripts. In order to use YUP, one needs to commit to becoming a YUP programmer.

该子项目是利用 NIH/NCRR 资助的中心拨款提供的资源的众多研究子项目之一。子项目和研究者 (PI) 可能已从另一个 NIH 来源获得主要资金，因此可以在其他 CRISP 条目中得到体现。列出的机构是中心的机构，不一定是研究者的机构。 Yammp 是一个通用分子力学程序，最初是为大分子系统的粗粒度建模而开发的，尽管我们已经使用 Yammp 解决了一些全原子问题。它最初应用于一系列不相关的问题（DNA 超螺旋、核糖体结构和模型膜的平均场模拟等）。随着对粗粒度模型的需求增长，我们决定将 Yammp 重写为一种形式 (Yammp2)，使其成为 Python 的扩展。结果是 YUP（Python 下的 Yammp），它具有对分子力学计算特别有用的附加数据类型。 YUP（Python 下的 Yammp）是 Python 的扩展，具有对分子力学计算特别有用的附加数据类型。因此，YUP 具有高度可编程性，这是它的主要优势。然而，用户会发现，YUP 比传统的分子力学程序需要更多的努力来学习，在传统的分子力学程序中，人们可以通过 GUI 或通过修改其他人的脚本来快速构建模型并运行模拟。为了使用 YUP，需要致力于成为一名 YUP 程序员。