pDynamoWiki is the wiki for the pDynamo program. It is place for the pDynamo users to cooperate, exchange information and experiment with ideas.

If you are a newcomer to pDynamo and are looking for information about its basic functionality and use, you should first look at Martin's book (warning: there have been a few changes since its publication) and the program's official web page, in particular the documentation, getting started and tutorials sections of the site. The library reference is also very useful for more expert users.

The material on this wiki is neither guaranteed nor meant to be completely bug-free, user-friendly and fool proof. It is simply a place where, for example, the pDynamo users can share their scripts to do a certain task (the Contributions section) or their QM or MM parameter files for specific systems (the Parameters section). In due course, once these scripts/parameters have been thoroughly tested and polished, they may eventually be "promoted" for inclusion within the official pDynamo distribution.

The Discussion section is meant especially for ongoing and future developments of the program: new features that it would be nice to include, who is doing what within the pDynamo community, etc.

Related Projects and Programs


GTKDynamo is a graphical user interface to pDynamo based on PyMOL, which is being developed by Jose Fernando Bachega.


Mikolaj Feliks suggests to take a look at this: bpython-interpreter.org.  It is a fancy interface to python which can autocomplete the names of functions, modules, arguments etc. This can really help explore and learn pDynamo.