The primary reference is the book by Martin J. Field, A Practical Introduction to the Simulation of Molecular Systems, 2007 [Amazon UK, Amazon US, CUP]. Additional documentation is available on text and on the Wiki.
The following material may be also installed and consulted:
- pDynamo-1.8.0 (everyone should install this)
- Introductory slides, Python basics and QC/MM basics.
- Pymol 1.6 (or higher)
- GTK Dynamo
- ORCA and introductory guide
- ORCA-pDynamo examples and tutorial
- Weighted ensemble: WESTPA and examples