Yammp Under Python (YUP), also known as Yammp 2, is a molecular modeling program. Although a general purpose tool, development is currently concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. YUP is based on an earlier program Yammp.


Information: About YUP: development philosophy, its intended use and overview of the program.
News: This section reports on the status of the project and contains development news. The final version of Yup.scx is available in YUP version 1.071201 and higher. Workshop (1): June 28 to July 1, 2005; Workshop (2): July 5 to 8, 2005; Workshop (3): August 16 to 18, 2005
Tan, R. K. Z., Petrov, A. S., Harvey, S. C. YUP: A Molecular Simulation Program for Coarse-Grained and Multiscaled Models. J. Chem. Theory Comput., 2006, 2(3), 529-540
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User Manual: How to use YUP to create a model and to carry out molecular mechanic simulations.
Technical Documentation: How to develop for new model types and new molecular mechanic methods. Programming in Python required.
Programming Manual: How to develop new potential energy terms. Programming in C/C++ required.


Download: YUP is available for PowerPC and x86 MacOSX and x86 and x86_64 LINUX systems. Latest Release: version 1.080827.
Tutorials: You can work through these exercises on your own or come to one of our Workshops.

iYUP: is a version of YUP that you can run from your web browser. The features are necessarily limited to those that can be presented in a web browser. To make interaction bearable, molecules are restricted in size and the duration of each simulation is limited to a few seconds.
Showcase: of work done with YUP, downloadable input files, scripts, graphics and movies. More or less a demo.
ETC: Miscellaneous.

The links above will bring you to sections of this site. At the bottom of every page in each section are a link back to this page and links to other sections of this site. The links below will bring you to other areas of this site and to other sites. YUP is being developed in the Harvey Laboratory in the School of Biology, Georgia Institute of Technology and is a component of the MMTSB at the Scripps Research Institute. The MMTSB link will open in a separate window.

Home: The Harvey Laboratory
Yammp: Ancestral version of YUP
MMTSB: Multiscale Modeling Tools In Structural Biology