REWRITING YAMMP

重写YAMMP

• 批准号: 7602258
• 负责人: STEPHEN C. HARVEY
• 金额: $ 6.37万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2008-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7602258
• 关键词: Cereals; Commit; Computer Retrieval of Information on Scientific Projects Database; Data; Funding; Grant; Institution; Learning; Modeling; Purpose; Pythons; Range; Research; Research Personnel; Resources; Ribosomes; Running; Source; Structure; Superhelical DNA; System; United States National Institutes of Health; membrane model; molecular mechanics; programs; simulation

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 peoples scripts. In order to use YUP, one needs to commit to becoming a YUP programmer.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 Yammp是一个通用的分子力学程序，最初是为大分子系统的粗颗粒建模而开发的，尽管我们已经用Yammp解决了一些全原子问题。它最初被应用于一系列不相关的问题（DNA超螺旋，核糖体的结构，以及模型膜上的平均场模拟等）。随着对粗粒度模型需求的增长，我们决定将Yammp重写为一种形式（Yammp 2），使其能够成为Python的扩展。结果是YUP（Yammp Under Python），它具有额外的数据类型，对分子力学计算特别有用。 YUP（Yammp Under Python）是Python的扩展，具有额外的数据类型，对分子力学计算特别有用。因此，YUP是高度可编程的，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或修改其他人来快速构建模型并运行模拟的脚本。为了使用YUP，你需要致力于成为一名YUP程序员。