MDX Tutorial
Getting Started Tinkering With MDX
Before proceeding through this tutorial, you should do the following:
- Download the MDX tarball and unpack it.
- Read through the README and NOTES files.
- Run the MDSim demo.
- Observe the basic subdirectory structure:
- mdx/arch/
- mdx/build/
- mdx/doc/
- mdx/doc/html/
- mdx/src/
- mdx/src/force/
- mdx/src/mdapi/
- mdx/src/mdio/
- mdx/src/step/
etc.
- Look through the MDX web documentation.
Caveats:
- The MDX libraries are still under active development and the interfaces will change in future releases.
- This tutorial will not work directly with MDX versions 1.1.x and later.
The tutorial works through the following questions:
- How do the MDX libraries work together
to complement each other?
(Specifically, we discuss libraries mdio, force, step, and their dependence on the definitions from mdapi/mdtypes.h.)
- How do I create my own module that
uses the libraries?
(We look over aspects of a small MD simulation program tinysim that depends on the previously discussed libraries.)
- How do I add a feature to "NAMD-lite"
(i.e. mdsim + deven)?
(We discuss modifying deven to compute and return linear momentum as a "result".)
