REWRITING YAMMP

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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.