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Here are the tutorials and reference documentation for DynamO.

All of the documentation of DynamO assumes the reader has some experience with both Linux and Molecular Dynamics simulation. There are some recommended resources listed below which will introduce the basics of these topics if you are at all unfamiliar with them.

Tutorials

1: Compiling DynamO from source
2: Introduction to DynamO
3: The configuration file
4: Thermostats and transport properties
5: Multiple species/interactions, compression dynamics, and ticker output plugins
6: Polydispersity, walls, granular dynamics, and a bit of python
A: Automatically processing output and config files

References

Configuration File Format Reference
Output Plugin Reference

FAQ

Frequently Asked Questions

DynamO Publications

If you find the DynamO useful and publish a paper using results obtained from DynamO, please help support it's development by citing the following paper.

M. N. Bannerman, R. Sargant, L. Lue, "DynamO: A free O(N) general event-driven simulator," J. Comp. Chem., 32, 3329-3338 (2011)

Below is an incomplete list of publications which have used DynamO:

If you have any publications you want to be listed here please contact the developers.

Recommended Resources

DynamO, like many Linux programs, is driven through a Command-Line Interface (CLI). To be able to use DynamO, you will need to be familiar with the Linux terminal. Take a look at this link to learn more about the terminal and how it works if you are at all unsure what this means.

If you're looking for general documentation on Molecular Dynamics, there are a few good introductory textbooks available. The definitive text by Allen and Tildesley has always been very popular with students and veterans alike.

"Computer Simulation of Liquids," M. P. Allen, and D. J. Tildesley, 1989, Oxford Science Pub.

A short summary of the basics, also written by Allen, is also available online if you cannot find a copy of the book.

Although the fundamentals of Molecular Dynamics are always the same, the event-driven techniques used in DynamO differ in implementation from the techniques described in the resources above. These differences are best described in the excellent book by Haile.

"Molecular Dynamics Simulation: Elementary Methods," J. M. Haile, 1992, Wiley

Page last modified: Sunday 1st February 2015