REWRITING YAMMP

本子项目是利用由NIH/NCRR资助的中心赠款提供的资源的众多研究子项目之一。子项目和研究者（PI）可能已经从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。列出的机构是中心的，不一定是研究者的机构。Yammp是一个通用的分子力学程序，最初是为大分子系统的粗粒度建模而开发的，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超卷曲、核糖体结构、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（Yammp2），使其能够成为Python的扩展。其结果是YUP (Python下的Yammp)，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。YUP因此是高度可编程的，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或修改其他人的脚本快速构建模型并运行模拟。为了使用YUP，一个人需要致力于成为YUP程序员。

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.