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;
July 5 to 8, 2005; Workshop (3): August 16
to 18, 2005
Reference: 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. Download PDF.
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
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.
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.