This program is used to generate coordinate files for use in molecular dynamics (MD) simulations of curved lipid bilayers
The BUMPy publication should be coming out shortly, stay tuned!
BUMPy is written and maintained by Kevin Boyd ([email protected]), in the lab of Eric May at the University of Connecticut.
No installation is necessary as long as you have a python (v3) interpreter
Just numpy!
BUMPY is designed to be used at the command line, with something like the command "python bumpy.py [ options ]". All you need is the bumpy.py file!
- For a description of command line options, use the -h option at the command line.
- For a list of supported curved shapes, use the --list option at the command line, or see the shape repository pdf.
- Example commands with BUMPy are available in the examples directory
- BUMPy is maintained on github (link: https://github.com/scal444/BUMPy)
- I'll happily accept code contributions to improve the tool or add shapes to the repository.
- If there's a shape you want to simulate, I can likely make a template for it very quickly. Email me with a description of what you want built and I'll add it to the repository.
To report bugs, email Kevin Boyd at [email protected]
- Templates used as starting structures for BUMPy need to contain WHOLE lipid molecules (ie - not broken across periodic boundaries)
- Template bilayers do NOT need to be large enough to wrap the flat bilayer into the desired shape; BUMPy will multiply the input laterally to create a flat bilayer of sufficient size. This does mean that the original box dimensions need to be correctly set
- All shapes are contained in the shapes class. The requirements for adding a shape to the repository are described in the shapes documentation
- Descriptions of supported shapes can be found in the shapes.pdf document. Note that for some shapes the terms "inner" and "outer" leaflets are ambiguous, so for those shapes a convention of "inner" and "outer" was chosen and is listed in the document. This convention does not change any of the pivotal-plane calculations.